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
> > [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/
> >> >
> >> > ---
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> >> > 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/
> >
> > ---
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> > To unsubscribe from this group and stop receiving emails from it, send
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> > email to aroma-affymetr...@googlegroups.com <javascript:>.
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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/
---
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