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_0.9.6 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.
>> >> >
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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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>
> --
> --
> 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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