Re: [aroma.affymetrix] 500K by doCRMAv2
On Mon, Jun 10, 2013 at 7:42 AM, Wei Tang tangwei1...@gmail.com wrote:
I have got to this step
doCBS(dsTTuple, ref=dsNTuple, verbose=-10)
Would you advise me what is the next? how to connect to the follow calling
CN step.
All you have to do is:
cns - CbsModel(dsTTuple, ref=dsNTuple);
fit(cns, verbose=verbose)
[Actually, doing CbsModel()+fit() is equivalent to calling doCBS(), so
you can skip doCBS() - doesn't matter].
ce - ChromosomeExplorer(cns)
process(ce, verbose=verbose)
another question, when I am doing allelic specific CN, I should follow
TumorBoost, right? Or, is there some changes?
You can follow the Paired PSCBS vignette online
[http://aroma-project.org/vignettes/PairedPSCBS-lowlevel]. By default
Paired PSCBS does TumorBoost normalization automatically before
segmentation. You should also be aware of the Paired PSCBS (PDF)
vignette that is part of the PSCBS package.
/Henrik
Many thanks,
Wei
On Thu, Jun 6, 2013 at 5:38 PM, Henrik Bengtsson
henrik.bengts...@aroma-project.org wrote:
On Thu, Jun 6, 2013 at 1:43 PM, Wei Tang tangwei1...@gmail.com wrote:
Everything goes very well. Nsp and Sty matched.
Great to hear.
BUT I forget to ask in which step should I pair the samples with tumor
and
normal. According to ,
Vignette: Paired total copy-number analysis
cns - CbsModel(dsT, dsN)
now I am using doCBS, how can I connect to the above step?
Good question. So, for the tumor-normal use case with multiple chip
types, you need to do a bit of manual setup first. Assuming your
tumors and normals are within the existing data set you use, here is
an illustration.
# General setup
dataSet - EC500K;
tags - ACC,-XY,BPN,-XY,RMA,A+B,FLN,-XY;
chipTypes - c(Mapping250K_Nsp, Mapping250K_Sty);
# Setup CRMAv2-generated data sets [this is what doCBS() does internally]
dsList - lapply(chipTypes, FUN=function(chipType) {
AromaUnitTotalCnBinarySet$byName(dataSet, tags=tags, chipType=chipType)
});
dsTuple - as.CopyNumberDataSetTuple(dsList);
# Try...
print(dsTuple);
# ...and check the array names that CBS match up.
print(getNames(dsTuple));
FYI, you could now launch the non-paired doCBS() as before using this
data-set tuple class:
doCBS(dsTuple, verbose=-10);
However, for the matched tumor-normal segmentation, you need to split
up your data-set tuple into a tumor and a normal one. Assuming you
know the indices of the samples in the above tuple as ordered by
getNames(dsTuple), you can do:
# Example:
idxsT - c(1:3, 6:7)
idxsN - c(4:5, 8:10)
dsTTuple - extract(dsTuple, idxsT);
dsNTuple - extract(dsTuple, idxsN);
# Verify you have the correct samples:
print(getNames(dsTTuple));
print(getNames(dsNTuple));
# Assert that they have the same number of samples:
# [doCBS() will do this too]
stopifnot(length(dsTTuple) == length(dsNTuple));
# Matched tumor-normal segmentation (pay attention to the verbose at
the beginning)
doCBS(dsTTuple, ref=dsNTuple, verbose=-10);
Hope this helps
Henrik
Many thanks,
Wei
On Wednesday, June 5, 2013 5:50:52 PM UTC-4, Henrik Bengtsson wrote:
JOn Wed, Jun 5, 2013 at 2:15 PM, Wei Tang tangw...@gmail.com wrote:
do they need to be the same names in 500K? How about SNP5, they are
additional samples.
Yes (I did write this in my long initial message). doCBS() identifies
which tuples of arrays belongs to which samples by matching up their
*names*, that is, by looking at:
getNames(dsC_EC500K_Nsp)
getNames(dsC_EC500K_Sty)
Note the difference between *names* and *full names* (cf.
http://aroma-project.org/definitions/namesAndTags). In your case the
*names* are:
getNames(dsC_EC500K_Sty)
[1] E1507T_STY E1510T_STY E1520T_STY ... SHE1796_STY
getNames(dsC_EC500K_Nsp)
[1] E1507T_Nsp E1510T_Nsp E1520T_Nsp ... SHE1796_NSP
Because of this, doCBS() fails to pair them up. So, yes, if they would
be:
getNames(dsC_EC500K_Sty)
[1] E1507T E1510T E1520T ... SHE1796
getNames(dsC_EC500K_Nsp)
[1] E1507T E1510T E1520T ... SHE1796
it would work as you expect. The *names* comes directly from the
*full names*, which by default comes from the *file names* (see above
link) Now, you don't have to rename the files to change the full
names. Instead you can use so called fullname translator function,
which will allow you to rename *full names* on the fly, cf.
http://aroma-project.org/howtos/setFullNamesTranslator. In your case
you'll only have to replace the underscores (_) with a comma (,) and
everything will work. So, do:
fnt - function(names, ...) gsub(_, ,, names, fixed=TRUE);
setFullNamesTranslator(dsC_EC500K_Sty, fnt);
setFullNamesTranslator(dsC_EC500K_Nsp, fnt);
and you should get:
getFullNames(dsC_EC500K_Sty)
[1] E1507T,STY,total E1510T,STY,total ... SHE1796,STY,total
getFullNames(dsC_EC500K_Nsp)
[1] E1507T,Nsp,total E1510T,Nsp,total ... SHE1796,NSP,total
and therefore:
Re: [aroma.affymetrix] 500K by doCRMAv2
Everything goes very well. Nsp and Sty matched. BUT I forget to ask in which step should I pair the samples with tumor and normal. According to , Vignette: Paired total copy-number analysis cns - CbsModel(dsT, dsN) now I am using doCBS, how can I connect to the above step? Many thanks, Wei On Wednesday, June 5, 2013 5:50:52 PM UTC-4, Henrik Bengtsson wrote: JOn Wed, Jun 5, 2013 at 2:15 PM, Wei Tang tangw...@gmail.comjavascript: wrote: do they need to be the same names in 500K? How about SNP5, they are additional samples. Yes (I did write this in my long initial message). doCBS() identifies which tuples of arrays belongs to which samples by matching up their *names*, that is, by looking at: getNames(dsC_EC500K_Nsp) getNames(dsC_EC500K_Sty) Note the difference between *names* and *full names* (cf. http://aroma-project.org/definitions/namesAndTags). In your case the *names* are: getNames(dsC_EC500K_Sty) [1] E1507T_STY E1510T_STY E1520T_STY ... SHE1796_STY getNames(dsC_EC500K_Nsp) [1] E1507T_Nsp E1510T_Nsp E1520T_Nsp ... SHE1796_NSP Because of this, doCBS() fails to pair them up. So, yes, if they would be: getNames(dsC_EC500K_Sty) [1] E1507T E1510T E1520T ... SHE1796 getNames(dsC_EC500K_Nsp) [1] E1507T E1510T E1520T ... SHE1796 it would work as you expect. The *names* comes directly from the *full names*, which by default comes from the *file names* (see above link) Now, you don't have to rename the files to change the full names. Instead you can use so called fullname translator function, which will allow you to rename *full names* on the fly, cf. http://aroma-project.org/howtos/setFullNamesTranslator. In your case you'll only have to replace the underscores (_) with a comma (,) and everything will work. So, do: fnt - function(names, ...) gsub(_, ,, names, fixed=TRUE); setFullNamesTranslator(dsC_EC500K_Sty, fnt); setFullNamesTranslator(dsC_EC500K_Nsp, fnt); and you should get: getFullNames(dsC_EC500K_Sty) [1] E1507T,STY,total E1510T,STY,total ... SHE1796,STY,total getFullNames(dsC_EC500K_Nsp) [1] E1507T,Nsp,total E1510T,Nsp,total ... SHE1796,NSP,total and therefore: getNames(dsC_EC500K_Sty) [1] E1507T E1510T ... SHE1796 getNames(dsC_EC500K_Nsp) [1] E1507T E1510T ... SHE1796 Then retry with doCBS(). If your GenomeWideSNP_5 arrays have completely different name formats, you have to create a more fancy full names translator function that takes the input names and translates them to match the above. Hope this helps Henrik On Wednesday, June 5, 2013 5:12:56 PM UTC-4, Wei Tang wrote: here you are print(getFullNames(dsC_EC500K_Sty)) [1] E1507T_STY,total E1510T_STY,total E1520T_STY,total [4] E1521T_STY,total E1532T_STY,total E1535T_STY,total [7] E1542T_STY,total E1546T_STY,total E1558T_STY,total [10] E1566T_STY,total E1572T_STY,total E1573T_STY,total [13] E1575T_STY,total E1584T_STY,total E1589T_STY,total [16] E1610T_STY,total E1635T_STY,total E1756T_STY,total [19] E1782T_STY,total E1796T_STY,total SHE1507_STY,total [22] SHE1510_STY,total SHE1520_STY,total SHE1521_STY,total [25] SHE1532_STY,total SHE1535_STY,total SHE1542_STY,total [28] SHE1546_STY,total SHE1558_STY,total SHE1566_STY,total [31] SHE1572_STY,total SHE1573_STY,total SHE1575_STY,total [34] SHE1584_STY,total SHE1589_STY,total SHE1610_STY,total [37] SHE1635_STY,total SHE1756_STY,total SHE1782_STY,total [40] SHE1796_STY,total print(getFullNames(dsC_EC500K_Nsp)) [1] E1507T_Nsp,total E1510T_Nsp,total E1520T_Nsp,total [4] E1521T_Nsp,total E1532T_Nsp,total E1535T_Nsp,total [7] E1542T_Nsp,total E1546T_Nsp,total E1558T_Nsp,total [10] E1566T_Nsp,total E1572T_Nsp,total E1573T_Nsp,total [13] E1575T_Nsp,total E1584T_Nsp,total E1589T_Nsp,total [16] E1610T_Nsp,total E1635T_Nsp,total E1756T_Nsp,total [19] E1782T_Nsp,total E1796T_Nsp,total SHE1507_NSP,total [22] SHE1510_NSP,total SHE1520_NSP,total SHE1521_NSP,total [25] SHE1532_NSP,total SHE1535_NSP,total SHE1542_NSP,total [28] SHE1546_NSP,total SHE1558_NSP,total SHE1566_NSP,total [31] SHE1572_NSP,total SHE1573_NSP,total SHE1575_NSP,total [34] SHE1584_NSP,total SHE1589_NSP,total SHE1610_NSP,total [37] SHE1635_NSP,total SHE1756_NSP,total SHE1782_NSP,total [40] SHE1796_NSP,total On Wednesday, June 5, 2013 5:01:19 PM UTC-4, Henrik Bengtsson wrote: On Wed, Jun 5, 2013 at 1:22 PM, Wei Tang tangw...@gmail.com wrote: Thank you, please see the info below. script dataSet_500K=EC500K dsC_EC500K_Sty=doCRMAv2(dataSet_500K,chipType=Mapping250K_Sty,verbose=verbose) dsC_EC500K_Nsp=doCRMAv2(dataSet_500K,chipType=Mapping250K_Nsp,verbose=verbose) dataSet=EC500K tags - ACC,-XY,BPN,-XY,RMA,A+B,FLN,-XY ## OR## tags - ACC,-XY,BPN,-XY,AVG,A+B,FLN,-XY res - doCBS(dataSet,
Re: [aroma.affymetrix] 500K by doCRMAv2
Hi Henrik , Thank you for you suggestion. but when I ran res - doCBS(dataSet, tags=tags, chipTypes=c(Mapping250K_Nsp, Mapping250K_Sty), verbose=verbose); it complained Error in file(pathname, open = rb) : invalid 'description' argument do you know how to fix it? my situation is all paired tumor-normal, 36 paired-samples in SNP5 and additional 20 paried-samples in 500K should I use Multi-source copy-number normalization and how about using doASCRMAv2, does the usage the same as doCRMAv2 ?; Many thanks, Wei On Thursday, May 30, 2013 6:05:55 PM UTC-4, Henrik Bengtsson wrote: Hi, I've done some updates to the help pages (e.g. ?doCBS), so before anything I recommend to update to aroma.core 2.9.5 and aroma.affymetrix 2.9.4: source(http://aroma-project.org/hbLite.R;); hbInstall(aroma.affymetrix); On Tue, May 28, 2013 at 9:37 AM, Wei Tang tangw...@gmail.comjavascript: wrote: Hi aroma.affymetrix developers, Before I start the analysis, I just want to confirm the CN analysis of 500K arrays with doCRMAv2, as I did not find a Vig specific about it. What I understand is, 1. run 250K_Nsp dsC_Nsp=doCRMAv2(test,cdf=Nsp,verbose=verbose) 2. run 250_Sty dsC_Sty=doCRMAv2(test,cdf=Sty,verbose=verbose) Yes, you can do CRMAv2 preprocessing for each chip type independently. However, for doCRMAv2() you need to do something like: dsC_Nsp - doCRMAv2(dataSet, chipType=Mapping250K_Nsp, verbose=verbose) dsC_Sty - doCRMAv2(dataSet, chipType=Mapping250K_Sty, verbose=verbose) Chip types have formal and strict names, cf. http://aroma-project.org/definitions/chipTypesAndCDFs 3. merge them together by aroma.cn Actually, despite its name, you don't need to aroma.cn package here. The basic CBS methods are still in the aroma.core package. So, after doing the above doCRMAv2() processing, you then want to do something like: tags - ACC,-XY,BPN,-XY,AVG,A+B,FLN,-XY; # Tags added by CRMAv2 res - doCBS(dataSet, tags=tags, chipTypes=c(Mapping250K_Nsp, Mapping250K_Sty), verbose=verbose); It's important that the array *names* of the Mapping250K_Nsp and Mapping250K_Sty pair up, because that is how doCBS() know which array files to pair up/merge in the segmentation. doCBS() match array names using the names from getNames(), e.g. names_Nsp - getNames(dsC_Nsp); names_Sty - getNames(dsC_Sty); If they don't match up, there are way to change the names so they do, cf. http://aroma-project.org/howtos/setFullNamesTranslator Would you mind telling me if I am correct with analysis? I also have SNP5.0 to merge, so should I merge 3 arrays at one time or, merge 500K first and then SNP5.0? You can just include them as a third chiptype set above, e.g. res - doCBS(dataSet, tags=tags, chipTypes=c(Mapping250K_Nsp, Mapping250K_Sty, GenomeWideSNP_5), verbose=verbose); Hope this helps/get you started /Henrik Thank you very much, Wei NCI/NIH -- -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups aroma.affymetrix group with website http://www.aroma-project.org/. To post to this group, send email to aroma-af...@googlegroups.comjavascript: To unsubscribe and other options, go to http://www.aroma-project.org/forum/ --- You received this message because you are subscribed to the Google Groups aroma.affymetrix group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetr...@googlegroups.com javascript:. For more options, visit https://groups.google.com/groups/opt_out. -- -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups aroma.affymetrix group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/ --- You received this message because you are subscribed to the Google Groups aroma.affymetrix group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/groups/opt_out.
Re: [aroma.affymetrix] 500K by doCRMAv2
Thank you, please see the info below. script dataSet_500K=EC500K dsC_EC500K_Sty=doCRMAv2(dataSet_500K,chipType=Mapping250K_Sty,verbose=verbose) dsC_EC500K_Nsp=doCRMAv2(dataSet_500K,chipType=Mapping250K_Nsp,verbose=verbose) dataSet=EC500K tags - ACC,-XY,BPN,-XY,RMA,A+B,FLN,-XY ## OR## tags - ACC,-XY,BPN,-XY,AVG,A+B,FLN,-XY res - doCBS(dataSet, tags=tags, chipTypes=c(Mapping250K_Nsp, Mapping250K_Sty), verbose=-10) traceback() 43: file(pathname, open = rb) 42: readRawFooter.AromaTabularBinaryFile(this) 41: readRawFooter(this) 40: readFooter.AromaTabularBinaryFile(this) 39: readFooter(this) 38: getChipType.AromaUnitSignalBinaryFile(getOneFile(this), ...) 37: getChipType(getOneFile(this), ...) 36: getChipType.AromaUnitSignalBinarySet(X[[1L]], ...) 35: FUN(X[[1L]], ...) 34: lapply(X = X, FUN = FUN, ...) 33: sapply(res, FUN = getChipType) 32: getSets.AromaMicroarrayDataSetTuple(this) 31: getSets(this) 30: getNames.GenericDataFileSetList(this, ...) 29: getNames(this, ...) 28: length.GenericDataFileSetList(refTuple) 27: length(refTuple) 26: isPaired.CopyNumberChromosomalModel(this) 25: isPaired(this) 24: getAsteriskTags.CopyNumberSegmentationModel(this) 23: getAsteriskTags(this) 22: paste(getAsteriskTags(this)[-1], collapse = ,) 21: getTags.CopyNumberSegmentationModel(this) 20: getTags(this) 19: paste(getTags(this), collapse = ,) 18: paste(Tags:, paste(getTags(this), collapse = ,)) 17: as.character.CopyNumberChromosomalModel(x) 16: as.character(x) 15: print(as.character(x)) 14: print.Object(...) 13: print(...) 12: eval(expr, envir, enclos) 11: eval(expr, pf) 10: withVisible(eval(expr, pf)) 9: evalVis(expr) 8: capture.Verbose(this, print(...), level = level) 7: capture(this, print(...), level = level) 6: print.Verbose(verbose, cbs) 5: print(verbose, cbs) 4: doCBS.CopyNumberDataSetTuple(dsTuple, arrays = arrays, ..., verbose = verbose) 3: doCBS(dsTuple, arrays = arrays, ..., verbose = verbose) 2: doCBS.default(dataSet, tags = tags, chipTypes = c(Mapping250K_Nsp, Mapping250K_Sty), verbose = -10) 1: doCBS(dataSet, tags = tags, chipTypes = c(Mapping250K_Nsp, Mapping250K_Sty), verbose = -10) sessionInfo() R version 3.0.0 (2013-04-03) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] R.cache_0.6.5 aroma.cn_1.3.3 DNAcopy_1.34.0 [4] aroma.affymetrix_2.9.4 affxparser_1.32.1 aroma.apd_0.2.3 [7] R.huge_0.4.1 aroma.light_1.30.2 aroma.core_2.9.5 [10] matrixStats_0.8.1 R.rsp_0.9.6R.devices_2.2.2 [13] R.filesets_2.0.1 R.utils_1.23.2 R.oo_1.13.6 [16] R.methodsS3_1.4.2 loaded via a namespace (and not attached): [1] PSCBS_0.34.8 digest_0.6.3 tools_3.0.0 On Wednesday, June 5, 2013 3:50:41 PM UTC-4, Henrik Bengtsson wrote: Hi. On Wed, Jun 5, 2013 at 11:31 AM, Wei Tang tangw...@gmail.comjavascript: wrote: Hi Henrik , Thank you for you suggestion. but when I ran res - doCBS(dataSet, tags=tags, chipTypes=c(Mapping250K_Nsp, Mapping250K_Sty), verbose=verbose); it complained Error in file(pathname, open = rb) : invalid 'description' argument do you know how to fix it? 1. What does traceback() output immediately after you get that error? 2. Can you show me your complete script? 3. What is your sessionInfo()? my situation is all paired tumor-normal, 36 paired-samples in SNP5 and additional 20 paried-samples in 500K should I use Multi-source copy-number normalization Possibly - depending on the amount of attenuation in the different chip type hybridizations (depends on date, lab etc) you may see a small improvement in power to detect change points. However, even without doing MSCN it is still always better to merge platforms (as doCBS() does) than running only single chips, cf. Figure 6 in H. Bengtsson, A. Ray, P. Spellman T.P. Speed, A single-sample method for normalizing and combining full-resolution copy numbers from multiple platforms, labs and analysis methods, Bioinformatics 2009 [http://aroma-project.org/publications]. and how about using doASCRMAv2, does the usage the same as doCRMAv2 ?; That's if you plan to infer parent-specific CNs. If you don't know yet, use doASCRMAv2(). Everything should work the same with doCBS(). /Henrik Many thanks, Wei On Thursday, May 30, 2013 6:05:55 PM UTC-4, Henrik Bengtsson wrote: Hi, I've done some updates to the help pages (e.g. ?doCBS), so before anything I recommend to update to aroma.core 2.9.5 and aroma.affymetrix 2.9.4: source(http://aroma-project.org/hbLite.R;); hbInstall(aroma.affymetrix); On Tue, May 28, 2013 at 9:37 AM, Wei Tang tangw...@gmail.com wrote: Hi aroma.affymetrix developers, Before I start the analysis, I just want to confirm the CN analysis of 500K arrays
Re: [aroma.affymetrix] 500K by doCRMAv2
On Wed, Jun 5, 2013 at 1:22 PM, Wei Tang tangwei1...@gmail.com wrote: Thank you, please see the info below. script dataSet_500K=EC500K dsC_EC500K_Sty=doCRMAv2(dataSet_500K,chipType=Mapping250K_Sty,verbose=verbose) dsC_EC500K_Nsp=doCRMAv2(dataSet_500K,chipType=Mapping250K_Nsp,verbose=verbose) dataSet=EC500K tags - ACC,-XY,BPN,-XY,RMA,A+B,FLN,-XY ## OR## tags - ACC,-XY,BPN,-XY,AVG,A+B,FLN,-XY res - doCBS(dataSet, tags=tags, chipTypes=c(Mapping250K_Nsp, Mapping250K_Sty), verbose=-10) Would you mind sharing the output of (all) the verbose output from the doCBS() call? That would help troubleshooting (I have a guess what's going on). It would also be useful to see the output of print(getFullNames(dsC_EC500K_Sty)) print(getFullNames(dsC_EC500K_Nsp)) If you don't want to share this on the mailing list, you can send it to me offline. /Henrik traceback() 43: file(pathname, open = rb) 42: readRawFooter.AromaTabularBinaryFile(this) 41: readRawFooter(this) 40: readFooter.AromaTabularBinaryFile(this) 39: readFooter(this) 38: getChipType.AromaUnitSignalBinaryFile(getOneFile(this), ...) 37: getChipType(getOneFile(this), ...) 36: getChipType.AromaUnitSignalBinarySet(X[[1L]], ...) 35: FUN(X[[1L]], ...) 34: lapply(X = X, FUN = FUN, ...) 33: sapply(res, FUN = getChipType) 32: getSets.AromaMicroarrayDataSetTuple(this) 31: getSets(this) 30: getNames.GenericDataFileSetList(this, ...) 29: getNames(this, ...) 28: length.GenericDataFileSetList(refTuple) 27: length(refTuple) 26: isPaired.CopyNumberChromosomalModel(this) 25: isPaired(this) 24: getAsteriskTags.CopyNumberSegmentationModel(this) 23: getAsteriskTags(this) 22: paste(getAsteriskTags(this)[-1], collapse = ,) 21: getTags.CopyNumberSegmentationModel(this) 20: getTags(this) 19: paste(getTags(this), collapse = ,) 18: paste(Tags:, paste(getTags(this), collapse = ,)) 17: as.character.CopyNumberChromosomalModel(x) 16: as.character(x) 15: print(as.character(x)) 14: print.Object(...) 13: print(...) 12: eval(expr, envir, enclos) 11: eval(expr, pf) 10: withVisible(eval(expr, pf)) 9: evalVis(expr) 8: capture.Verbose(this, print(...), level = level) 7: capture(this, print(...), level = level) 6: print.Verbose(verbose, cbs) 5: print(verbose, cbs) 4: doCBS.CopyNumberDataSetTuple(dsTuple, arrays = arrays, ..., verbose = verbose) 3: doCBS(dsTuple, arrays = arrays, ..., verbose = verbose) 2: doCBS.default(dataSet, tags = tags, chipTypes = c(Mapping250K_Nsp, Mapping250K_Sty), verbose = -10) 1: doCBS(dataSet, tags = tags, chipTypes = c(Mapping250K_Nsp, Mapping250K_Sty), verbose = -10) sessionInfo() R version 3.0.0 (2013-04-03) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] R.cache_0.6.5 aroma.cn_1.3.3 DNAcopy_1.34.0 [4] aroma.affymetrix_2.9.4 affxparser_1.32.1 aroma.apd_0.2.3 [7] R.huge_0.4.1 aroma.light_1.30.2 aroma.core_2.9.5 [10] matrixStats_0.8.1 R.rsp_0.9.6R.devices_2.2.2 [13] R.filesets_2.0.1 R.utils_1.23.2 R.oo_1.13.6 [16] R.methodsS3_1.4.2 loaded via a namespace (and not attached): [1] PSCBS_0.34.8 digest_0.6.3 tools_3.0.0 On Wednesday, June 5, 2013 3:50:41 PM UTC-4, Henrik Bengtsson wrote: Hi. On Wed, Jun 5, 2013 at 11:31 AM, Wei Tang tangw...@gmail.com wrote: Hi Henrik , Thank you for you suggestion. but when I ran res - doCBS(dataSet, tags=tags, chipTypes=c(Mapping250K_Nsp, Mapping250K_Sty), verbose=verbose); it complained Error in file(pathname, open = rb) : invalid 'description' argument do you know how to fix it? 1. What does traceback() output immediately after you get that error? 2. Can you show me your complete script? 3. What is your sessionInfo()? my situation is all paired tumor-normal, 36 paired-samples in SNP5 and additional 20 paried-samples in 500K should I use Multi-source copy-number normalization Possibly - depending on the amount of attenuation in the different chip type hybridizations (depends on date, lab etc) you may see a small improvement in power to detect change points. However, even without doing MSCN it is still always better to merge platforms (as doCBS() does) than running only single chips, cf. Figure 6 in H. Bengtsson, A. Ray, P. Spellman T.P. Speed, A single-sample method for normalizing and combining full-resolution copy numbers from multiple platforms, labs and analysis methods, Bioinformatics 2009 [http://aroma-project.org/publications]. and how about using doASCRMAv2, does the usage the same as doCRMAv2 ?; That's if you plan to infer parent-specific CNs. If you don't know yet, use doASCRMAv2(). Everything should work the same with doCBS(). /Henrik Many thanks, Wei On Thursday, May 30, 2013 6:05:55 PM UTC-4, Henrik Bengtsson wrote: Hi, I've
Re: [aroma.affymetrix] 500K by doCRMAv2
here you are print(getFullNames(dsC_EC500K_Sty)) [1] E1507T_STY,total E1510T_STY,total E1520T_STY,total [4] E1521T_STY,total E1532T_STY,total E1535T_STY,total [7] E1542T_STY,total E1546T_STY,total E1558T_STY,total [10] E1566T_STY,total E1572T_STY,total E1573T_STY,total [13] E1575T_STY,total E1584T_STY,total E1589T_STY,total [16] E1610T_STY,total E1635T_STY,total E1756T_STY,total [19] E1782T_STY,total E1796T_STY,total SHE1507_STY,total [22] SHE1510_STY,total SHE1520_STY,total SHE1521_STY,total [25] SHE1532_STY,total SHE1535_STY,total SHE1542_STY,total [28] SHE1546_STY,total SHE1558_STY,total SHE1566_STY,total [31] SHE1572_STY,total SHE1573_STY,total SHE1575_STY,total [34] SHE1584_STY,total SHE1589_STY,total SHE1610_STY,total [37] SHE1635_STY,total SHE1756_STY,total SHE1782_STY,total [40] SHE1796_STY,total print(getFullNames(dsC_EC500K_Nsp)) [1] E1507T_Nsp,total E1510T_Nsp,total E1520T_Nsp,total [4] E1521T_Nsp,total E1532T_Nsp,total E1535T_Nsp,total [7] E1542T_Nsp,total E1546T_Nsp,total E1558T_Nsp,total [10] E1566T_Nsp,total E1572T_Nsp,total E1573T_Nsp,total [13] E1575T_Nsp,total E1584T_Nsp,total E1589T_Nsp,total [16] E1610T_Nsp,total E1635T_Nsp,total E1756T_Nsp,total [19] E1782T_Nsp,total E1796T_Nsp,total SHE1507_NSP,total [22] SHE1510_NSP,total SHE1520_NSP,total SHE1521_NSP,total [25] SHE1532_NSP,total SHE1535_NSP,total SHE1542_NSP,total [28] SHE1546_NSP,total SHE1558_NSP,total SHE1566_NSP,total [31] SHE1572_NSP,total SHE1573_NSP,total SHE1575_NSP,total [34] SHE1584_NSP,total SHE1589_NSP,total SHE1610_NSP,total [37] SHE1635_NSP,total SHE1756_NSP,total SHE1782_NSP,total [40] SHE1796_NSP,total On Wednesday, June 5, 2013 5:01:19 PM UTC-4, Henrik Bengtsson wrote: On Wed, Jun 5, 2013 at 1:22 PM, Wei Tang tangw...@gmail.com javascript: wrote: Thank you, please see the info below. script dataSet_500K=EC500K dsC_EC500K_Sty=doCRMAv2(dataSet_500K,chipType=Mapping250K_Sty,verbose=verbose) dsC_EC500K_Nsp=doCRMAv2(dataSet_500K,chipType=Mapping250K_Nsp,verbose=verbose) dataSet=EC500K tags - ACC,-XY,BPN,-XY,RMA,A+B,FLN,-XY ## OR## tags - ACC,-XY,BPN,-XY,AVG,A+B,FLN,-XY res - doCBS(dataSet, tags=tags, chipTypes=c(Mapping250K_Nsp, Mapping250K_Sty), verbose=-10) Would you mind sharing the output of (all) the verbose output from the doCBS() call? That would help troubleshooting (I have a guess what's going on). It would also be useful to see the output of print(getFullNames(dsC_EC500K_Sty)) print(getFullNames(dsC_EC500K_Nsp)) If you don't want to share this on the mailing list, you can send it to me offline. /Henrik traceback() 43: file(pathname, open = rb) 42: readRawFooter.AromaTabularBinaryFile(this) 41: readRawFooter(this) 40: readFooter.AromaTabularBinaryFile(this) 39: readFooter(this) 38: getChipType.AromaUnitSignalBinaryFile(getOneFile(this), ...) 37: getChipType(getOneFile(this), ...) 36: getChipType.AromaUnitSignalBinarySet(X[[1L]], ...) 35: FUN(X[[1L]], ...) 34: lapply(X = X, FUN = FUN, ...) 33: sapply(res, FUN = getChipType) 32: getSets.AromaMicroarrayDataSetTuple(this) 31: getSets(this) 30: getNames.GenericDataFileSetList(this, ...) 29: getNames(this, ...) 28: length.GenericDataFileSetList(refTuple) 27: length(refTuple) 26: isPaired.CopyNumberChromosomalModel(this) 25: isPaired(this) 24: getAsteriskTags.CopyNumberSegmentationModel(this) 23: getAsteriskTags(this) 22: paste(getAsteriskTags(this)[-1], collapse = ,) 21: getTags.CopyNumberSegmentationModel(this) 20: getTags(this) 19: paste(getTags(this), collapse = ,) 18: paste(Tags:, paste(getTags(this), collapse = ,)) 17: as.character.CopyNumberChromosomalModel(x) 16: as.character(x) 15: print(as.character(x)) 14: print.Object(...) 13: print(...) 12: eval(expr, envir, enclos) 11: eval(expr, pf) 10: withVisible(eval(expr, pf)) 9: evalVis(expr) 8: capture.Verbose(this, print(...), level = level) 7: capture(this, print(...), level = level) 6: print.Verbose(verbose, cbs) 5: print(verbose, cbs) 4: doCBS.CopyNumberDataSetTuple(dsTuple, arrays = arrays, ..., verbose = verbose) 3: doCBS(dsTuple, arrays = arrays, ..., verbose = verbose) 2: doCBS.default(dataSet, tags = tags, chipTypes = c(Mapping250K_Nsp, Mapping250K_Sty), verbose = -10) 1: doCBS(dataSet, tags = tags, chipTypes = c(Mapping250K_Nsp, Mapping250K_Sty), verbose = -10) sessionInfo() R version 3.0.0 (2013-04-03) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] R.cache_0.6.5 aroma.cn_1.3.3 DNAcopy_1.34.0 [4] aroma.affymetrix_2.9.4 affxparser_1.32.1 aroma.apd_0.2.3 [7] R.huge_0.4.1 aroma.light_1.30.2 aroma.core_2.9.5
Re: [aroma.affymetrix] 500K by doCRMAv2
do they need to be the same names in 500K? How about SNP5, they are additional samples. On Wednesday, June 5, 2013 5:12:56 PM UTC-4, Wei Tang wrote: here you are print(getFullNames(dsC_EC500K_Sty)) [1] E1507T_STY,total E1510T_STY,total E1520T_STY,total [4] E1521T_STY,total E1532T_STY,total E1535T_STY,total [7] E1542T_STY,total E1546T_STY,total E1558T_STY,total [10] E1566T_STY,total E1572T_STY,total E1573T_STY,total [13] E1575T_STY,total E1584T_STY,total E1589T_STY,total [16] E1610T_STY,total E1635T_STY,total E1756T_STY,total [19] E1782T_STY,total E1796T_STY,total SHE1507_STY,total [22] SHE1510_STY,total SHE1520_STY,total SHE1521_STY,total [25] SHE1532_STY,total SHE1535_STY,total SHE1542_STY,total [28] SHE1546_STY,total SHE1558_STY,total SHE1566_STY,total [31] SHE1572_STY,total SHE1573_STY,total SHE1575_STY,total [34] SHE1584_STY,total SHE1589_STY,total SHE1610_STY,total [37] SHE1635_STY,total SHE1756_STY,total SHE1782_STY,total [40] SHE1796_STY,total print(getFullNames(dsC_EC500K_Nsp)) [1] E1507T_Nsp,total E1510T_Nsp,total E1520T_Nsp,total [4] E1521T_Nsp,total E1532T_Nsp,total E1535T_Nsp,total [7] E1542T_Nsp,total E1546T_Nsp,total E1558T_Nsp,total [10] E1566T_Nsp,total E1572T_Nsp,total E1573T_Nsp,total [13] E1575T_Nsp,total E1584T_Nsp,total E1589T_Nsp,total [16] E1610T_Nsp,total E1635T_Nsp,total E1756T_Nsp,total [19] E1782T_Nsp,total E1796T_Nsp,total SHE1507_NSP,total [22] SHE1510_NSP,total SHE1520_NSP,total SHE1521_NSP,total [25] SHE1532_NSP,total SHE1535_NSP,total SHE1542_NSP,total [28] SHE1546_NSP,total SHE1558_NSP,total SHE1566_NSP,total [31] SHE1572_NSP,total SHE1573_NSP,total SHE1575_NSP,total [34] SHE1584_NSP,total SHE1589_NSP,total SHE1610_NSP,total [37] SHE1635_NSP,total SHE1756_NSP,total SHE1782_NSP,total [40] SHE1796_NSP,total On Wednesday, June 5, 2013 5:01:19 PM UTC-4, Henrik Bengtsson wrote: On Wed, Jun 5, 2013 at 1:22 PM, Wei Tang tangw...@gmail.com wrote: Thank you, please see the info below. script dataSet_500K=EC500K dsC_EC500K_Sty=doCRMAv2(dataSet_500K,chipType=Mapping250K_Sty,verbose=verbose) dsC_EC500K_Nsp=doCRMAv2(dataSet_500K,chipType=Mapping250K_Nsp,verbose=verbose) dataSet=EC500K tags - ACC,-XY,BPN,-XY,RMA,A+B,FLN,-XY ## OR## tags - ACC,-XY,BPN,-XY,AVG,A+B,FLN,-XY res - doCBS(dataSet, tags=tags, chipTypes=c(Mapping250K_Nsp, Mapping250K_Sty), verbose=-10) Would you mind sharing the output of (all) the verbose output from the doCBS() call? That would help troubleshooting (I have a guess what's going on). It would also be useful to see the output of print(getFullNames(dsC_EC500K_Sty)) print(getFullNames(dsC_EC500K_Nsp)) If you don't want to share this on the mailing list, you can send it to me offline. /Henrik traceback() 43: file(pathname, open = rb) 42: readRawFooter.AromaTabularBinaryFile(this) 41: readRawFooter(this) 40: readFooter.AromaTabularBinaryFile(this) 39: readFooter(this) 38: getChipType.AromaUnitSignalBinaryFile(getOneFile(this), ...) 37: getChipType(getOneFile(this), ...) 36: getChipType.AromaUnitSignalBinarySet(X[[1L]], ...) 35: FUN(X[[1L]], ...) 34: lapply(X = X, FUN = FUN, ...) 33: sapply(res, FUN = getChipType) 32: getSets.AromaMicroarrayDataSetTuple(this) 31: getSets(this) 30: getNames.GenericDataFileSetList(this, ...) 29: getNames(this, ...) 28: length.GenericDataFileSetList(refTuple) 27: length(refTuple) 26: isPaired.CopyNumberChromosomalModel(this) 25: isPaired(this) 24: getAsteriskTags.CopyNumberSegmentationModel(this) 23: getAsteriskTags(this) 22: paste(getAsteriskTags(this)[-1], collapse = ,) 21: getTags.CopyNumberSegmentationModel(this) 20: getTags(this) 19: paste(getTags(this), collapse = ,) 18: paste(Tags:, paste(getTags(this), collapse = ,)) 17: as.character.CopyNumberChromosomalModel(x) 16: as.character(x) 15: print(as.character(x)) 14: print.Object(...) 13: print(...) 12: eval(expr, envir, enclos) 11: eval(expr, pf) 10: withVisible(eval(expr, pf)) 9: evalVis(expr) 8: capture.Verbose(this, print(...), level = level) 7: capture(this, print(...), level = level) 6: print.Verbose(verbose, cbs) 5: print(verbose, cbs) 4: doCBS.CopyNumberDataSetTuple(dsTuple, arrays = arrays, ..., verbose = verbose) 3: doCBS(dsTuple, arrays = arrays, ..., verbose = verbose) 2: doCBS.default(dataSet, tags = tags, chipTypes = c(Mapping250K_Nsp, Mapping250K_Sty), verbose = -10) 1: doCBS(dataSet, tags = tags, chipTypes = c(Mapping250K_Nsp, Mapping250K_Sty), verbose = -10) sessionInfo() R version 3.0.0 (2013-04-03) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] R.cache_0.6.5
Re: [aroma.affymetrix] 500K by doCRMAv2
JOn Wed, Jun 5, 2013 at 2:15 PM, Wei Tang tangwei1...@gmail.com wrote: do they need to be the same names in 500K? How about SNP5, they are additional samples. Yes (I did write this in my long initial message). doCBS() identifies which tuples of arrays belongs to which samples by matching up their *names*, that is, by looking at: getNames(dsC_EC500K_Nsp) getNames(dsC_EC500K_Sty) Note the difference between *names* and *full names* (cf. http://aroma-project.org/definitions/namesAndTags). In your case the *names* are: getNames(dsC_EC500K_Sty) [1] E1507T_STY E1510T_STY E1520T_STY ... SHE1796_STY getNames(dsC_EC500K_Nsp) [1] E1507T_Nsp E1510T_Nsp E1520T_Nsp ... SHE1796_NSP Because of this, doCBS() fails to pair them up. So, yes, if they would be: getNames(dsC_EC500K_Sty) [1] E1507T E1510T E1520T ... SHE1796 getNames(dsC_EC500K_Nsp) [1] E1507T E1510T E1520T ... SHE1796 it would work as you expect. The *names* comes directly from the *full names*, which by default comes from the *file names* (see above link) Now, you don't have to rename the files to change the full names. Instead you can use so called fullname translator function, which will allow you to rename *full names* on the fly, cf. http://aroma-project.org/howtos/setFullNamesTranslator. In your case you'll only have to replace the underscores (_) with a comma (,) and everything will work. So, do: fnt - function(names, ...) gsub(_, ,, names, fixed=TRUE); setFullNamesTranslator(dsC_EC500K_Sty, fnt); setFullNamesTranslator(dsC_EC500K_Nsp, fnt); and you should get: getFullNames(dsC_EC500K_Sty) [1] E1507T,STY,total E1510T,STY,total ... SHE1796,STY,total getFullNames(dsC_EC500K_Nsp) [1] E1507T,Nsp,total E1510T,Nsp,total ... SHE1796,NSP,total and therefore: getNames(dsC_EC500K_Sty) [1] E1507T E1510T ... SHE1796 getNames(dsC_EC500K_Nsp) [1] E1507T E1510T ... SHE1796 Then retry with doCBS(). If your GenomeWideSNP_5 arrays have completely different name formats, you have to create a more fancy full names translator function that takes the input names and translates them to match the above. Hope this helps Henrik On Wednesday, June 5, 2013 5:12:56 PM UTC-4, Wei Tang wrote: here you are print(getFullNames(dsC_EC500K_Sty)) [1] E1507T_STY,total E1510T_STY,total E1520T_STY,total [4] E1521T_STY,total E1532T_STY,total E1535T_STY,total [7] E1542T_STY,total E1546T_STY,total E1558T_STY,total [10] E1566T_STY,total E1572T_STY,total E1573T_STY,total [13] E1575T_STY,total E1584T_STY,total E1589T_STY,total [16] E1610T_STY,total E1635T_STY,total E1756T_STY,total [19] E1782T_STY,total E1796T_STY,total SHE1507_STY,total [22] SHE1510_STY,total SHE1520_STY,total SHE1521_STY,total [25] SHE1532_STY,total SHE1535_STY,total SHE1542_STY,total [28] SHE1546_STY,total SHE1558_STY,total SHE1566_STY,total [31] SHE1572_STY,total SHE1573_STY,total SHE1575_STY,total [34] SHE1584_STY,total SHE1589_STY,total SHE1610_STY,total [37] SHE1635_STY,total SHE1756_STY,total SHE1782_STY,total [40] SHE1796_STY,total print(getFullNames(dsC_EC500K_Nsp)) [1] E1507T_Nsp,total E1510T_Nsp,total E1520T_Nsp,total [4] E1521T_Nsp,total E1532T_Nsp,total E1535T_Nsp,total [7] E1542T_Nsp,total E1546T_Nsp,total E1558T_Nsp,total [10] E1566T_Nsp,total E1572T_Nsp,total E1573T_Nsp,total [13] E1575T_Nsp,total E1584T_Nsp,total E1589T_Nsp,total [16] E1610T_Nsp,total E1635T_Nsp,total E1756T_Nsp,total [19] E1782T_Nsp,total E1796T_Nsp,total SHE1507_NSP,total [22] SHE1510_NSP,total SHE1520_NSP,total SHE1521_NSP,total [25] SHE1532_NSP,total SHE1535_NSP,total SHE1542_NSP,total [28] SHE1546_NSP,total SHE1558_NSP,total SHE1566_NSP,total [31] SHE1572_NSP,total SHE1573_NSP,total SHE1575_NSP,total [34] SHE1584_NSP,total SHE1589_NSP,total SHE1610_NSP,total [37] SHE1635_NSP,total SHE1756_NSP,total SHE1782_NSP,total [40] SHE1796_NSP,total On Wednesday, June 5, 2013 5:01:19 PM UTC-4, Henrik Bengtsson wrote: On Wed, Jun 5, 2013 at 1:22 PM, Wei Tang tangw...@gmail.com wrote: Thank you, please see the info below. script dataSet_500K=EC500K dsC_EC500K_Sty=doCRMAv2(dataSet_500K,chipType=Mapping250K_Sty,verbose=verbose) dsC_EC500K_Nsp=doCRMAv2(dataSet_500K,chipType=Mapping250K_Nsp,verbose=verbose) dataSet=EC500K tags - ACC,-XY,BPN,-XY,RMA,A+B,FLN,-XY ## OR## tags - ACC,-XY,BPN,-XY,AVG,A+B,FLN,-XY res - doCBS(dataSet, tags=tags, chipTypes=c(Mapping250K_Nsp, Mapping250K_Sty), verbose=-10) Would you mind sharing the output of (all) the verbose output from the doCBS() call? That would help troubleshooting (I have a guess what's going on). It would also be useful to see the output of print(getFullNames(dsC_EC500K_Sty)) print(getFullNames(dsC_EC500K_Nsp)) If you don't want to share this on the mailing list, you can send it to me offline. /Henrik traceback() 43: file(pathname, open = rb) 42: readRawFooter.AromaTabularBinaryFile(this) 41: readRawFooter(this) 40:
Re: [aroma.affymetrix] 500K by doCRMAv2
Thank you so much for your guidance and really smart move for name translator. I think I should be able to make it this time. On Wednesday, June 5, 2013 5:50:52 PM UTC-4, Henrik Bengtsson wrote: JOn Wed, Jun 5, 2013 at 2:15 PM, Wei Tang tangw...@gmail.comjavascript: wrote: do they need to be the same names in 500K? How about SNP5, they are additional samples. Yes (I did write this in my long initial message). doCBS() identifies which tuples of arrays belongs to which samples by matching up their *names*, that is, by looking at: getNames(dsC_EC500K_Nsp) getNames(dsC_EC500K_Sty) Note the difference between *names* and *full names* (cf. http://aroma-project.org/definitions/namesAndTags). In your case the *names* are: getNames(dsC_EC500K_Sty) [1] E1507T_STY E1510T_STY E1520T_STY ... SHE1796_STY getNames(dsC_EC500K_Nsp) [1] E1507T_Nsp E1510T_Nsp E1520T_Nsp ... SHE1796_NSP Because of this, doCBS() fails to pair them up. So, yes, if they would be: getNames(dsC_EC500K_Sty) [1] E1507T E1510T E1520T ... SHE1796 getNames(dsC_EC500K_Nsp) [1] E1507T E1510T E1520T ... SHE1796 it would work as you expect. The *names* comes directly from the *full names*, which by default comes from the *file names* (see above link) Now, you don't have to rename the files to change the full names. Instead you can use so called fullname translator function, which will allow you to rename *full names* on the fly, cf. http://aroma-project.org/howtos/setFullNamesTranslator. In your case you'll only have to replace the underscores (_) with a comma (,) and everything will work. So, do: fnt - function(names, ...) gsub(_, ,, names, fixed=TRUE); setFullNamesTranslator(dsC_EC500K_Sty, fnt); setFullNamesTranslator(dsC_EC500K_Nsp, fnt); and you should get: getFullNames(dsC_EC500K_Sty) [1] E1507T,STY,total E1510T,STY,total ... SHE1796,STY,total getFullNames(dsC_EC500K_Nsp) [1] E1507T,Nsp,total E1510T,Nsp,total ... SHE1796,NSP,total and therefore: getNames(dsC_EC500K_Sty) [1] E1507T E1510T ... SHE1796 getNames(dsC_EC500K_Nsp) [1] E1507T E1510T ... SHE1796 Then retry with doCBS(). If your GenomeWideSNP_5 arrays have completely different name formats, you have to create a more fancy full names translator function that takes the input names and translates them to match the above. Hope this helps Henrik On Wednesday, June 5, 2013 5:12:56 PM UTC-4, Wei Tang wrote: here you are print(getFullNames(dsC_EC500K_Sty)) [1] E1507T_STY,total E1510T_STY,total E1520T_STY,total [4] E1521T_STY,total E1532T_STY,total E1535T_STY,total [7] E1542T_STY,total E1546T_STY,total E1558T_STY,total [10] E1566T_STY,total E1572T_STY,total E1573T_STY,total [13] E1575T_STY,total E1584T_STY,total E1589T_STY,total [16] E1610T_STY,total E1635T_STY,total E1756T_STY,total [19] E1782T_STY,total E1796T_STY,total SHE1507_STY,total [22] SHE1510_STY,total SHE1520_STY,total SHE1521_STY,total [25] SHE1532_STY,total SHE1535_STY,total SHE1542_STY,total [28] SHE1546_STY,total SHE1558_STY,total SHE1566_STY,total [31] SHE1572_STY,total SHE1573_STY,total SHE1575_STY,total [34] SHE1584_STY,total SHE1589_STY,total SHE1610_STY,total [37] SHE1635_STY,total SHE1756_STY,total SHE1782_STY,total [40] SHE1796_STY,total print(getFullNames(dsC_EC500K_Nsp)) [1] E1507T_Nsp,total E1510T_Nsp,total E1520T_Nsp,total [4] E1521T_Nsp,total E1532T_Nsp,total E1535T_Nsp,total [7] E1542T_Nsp,total E1546T_Nsp,total E1558T_Nsp,total [10] E1566T_Nsp,total E1572T_Nsp,total E1573T_Nsp,total [13] E1575T_Nsp,total E1584T_Nsp,total E1589T_Nsp,total [16] E1610T_Nsp,total E1635T_Nsp,total E1756T_Nsp,total [19] E1782T_Nsp,total E1796T_Nsp,total SHE1507_NSP,total [22] SHE1510_NSP,total SHE1520_NSP,total SHE1521_NSP,total [25] SHE1532_NSP,total SHE1535_NSP,total SHE1542_NSP,total [28] SHE1546_NSP,total SHE1558_NSP,total SHE1566_NSP,total [31] SHE1572_NSP,total SHE1573_NSP,total SHE1575_NSP,total [34] SHE1584_NSP,total SHE1589_NSP,total SHE1610_NSP,total [37] SHE1635_NSP,total SHE1756_NSP,total SHE1782_NSP,total [40] SHE1796_NSP,total On Wednesday, June 5, 2013 5:01:19 PM UTC-4, Henrik Bengtsson wrote: On Wed, Jun 5, 2013 at 1:22 PM, Wei Tang tangw...@gmail.com wrote: Thank you, please see the info below. script dataSet_500K=EC500K dsC_EC500K_Sty=doCRMAv2(dataSet_500K,chipType=Mapping250K_Sty,verbose=verbose) dsC_EC500K_Nsp=doCRMAv2(dataSet_500K,chipType=Mapping250K_Nsp,verbose=verbose) dataSet=EC500K tags - ACC,-XY,BPN,-XY,RMA,A+B,FLN,-XY ## OR## tags - ACC,-XY,BPN,-XY,AVG,A+B,FLN,-XY res - doCBS(dataSet, tags=tags, chipTypes=c(Mapping250K_Nsp, Mapping250K_Sty), verbose=-10) Would you mind sharing the output of (all) the verbose output from the doCBS() call?
