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.com<javascript:>> > 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: 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_0.9.6 R.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 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 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.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-affymetr...@googlegroups.com. > >>> >> >> > 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-af...@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-affymetr...@googlegroups.com. > >>> >> > 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-af...@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-affymetr...@googlegroups.com. > >>> > 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-af...@googlegroups.com<javascript:> > > 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. 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