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:
>>
>> > 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
>> >>> >> >> >
>> >>> >> >> >
>> >>> >> >> >
>> >>> >> >> > --
>> >>> >> >> > --
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>> >>> >> >> > run
>> >>> >> >> > the
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>> >>> >> >> > sessionInfo()
>> >>> >> >> > and
>> >>> >> >> > traceback(), and 3) to post a complete code example.
>> >>> >> >> >
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>> >>> >> > --
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>> >>> >> > the
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>
> --
> --
> 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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>
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--
--
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.
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