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 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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>> >> >> >
>> >> >> >
>> >> >
>> >> > --
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>> latest
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