Dear Henrik,
thank you so much for your complete answer! I'll try your suggestions on
monday and give you some feedback!
Best,
Xavi.
2011/6/17 Henrik Bengtsson <henrik.bengts...@aroma-project.org>
> Hi.
>
> On Thu, Jun 16, 2011 at 9:52 AM, Xavi Sole <xavier.s...@gmail.com> wrote:
> > Hi all,
> > I have successfully performed CRMAv2 on a set of ~200 Affy 6.0 samples. I
> > have tumor and normal samples, and now I want to apply an unpaired CBS
> > model. I know ho to do the paired model, but I'm not sure is this code is
> > right for the unpaired one:
> > library(aroma.affymetrix);
> > library(aroma.cn);
>
> No need for 'aroma.cn' here.
>
> > verbose <- Arguments$getVerbose(-8, timestamp=TRUE);
> > options(digits=4);
> > setOption(aromaSettings, "memory/ram", 500.0)
> > # Verify that the data set can be located:
> > cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_6", tags="Full");
> > dataSet <- "CEL_files";
>
> Each analysis you run should have a unique data set name, i.e. what
> name should you use next time? I recommend to use a much more
> informative name of your data set - something that reflects the
> project name and/or the investigator and the year, or similar.
>
> > dsR <- AffymetrixCelSet$byName(dataSet, cdf=cdf);
> > setFullName(dsR, dataSet);
>
> No need to do this.
>
> > # Using CRMAv2
> > dsList <- doCRMAv2(dataSet, cdf=cdf, combineAlleles=FALSE,
> verbose=verbose);
>
> Since you've already have setup an AffymetrixCelSet object ('dsR')
> above, you should use that instead:
>
> dsList <- doCRMAv2(dsR, combineAlleles=FALSE, verbose=verbose);
>
> or even shorter for allele-specific analysis, you can equivalently do:
>
> dsList <- doASCRMAv2(dsR, verbose=verbose);
>
> > dsC <- dsList$total;
> > # Splitting the dataset in normal-tumor pairs
> > infoSamples <- read.table("samples.txt", sep="\t", header=TRUE, as.is
> =TRUE,
> > strip.white=TRUE);
> > #Rows in this file are in the same order as arrays in the aroma dataset.
> > idxN <- which(infoSamples$type=="Normal");
> > idxT <- which(infoSamples$type=="Tumor");
>
> This is a bit dangerous since it assumes that the rows in your
> 'samples.txt' file is ordered the same way as the files on this. At
> least I would assert that that is the case by something like:
>
> stopifnot(all(infoSamples$name == getName(dsC));
>
> or similar.
>
> > dsN <- extract(dsC, idxN);
> > dsT <- extract(dsC, idxT);
> > # Circular binary segmentation T vs N: Paired model (first N sample pairs
> > with first T sample)
> > cns <- CbsModel(dsT, dsN);
> > fit(cns, verbose=TRUE);
> > regDatList <- getRegions(cns);
>
> Yes, this does a tumor-normal paired CBS segmentation (and extracts
> the table of regions afterward).
>
> > # Circular binary segmentation T vs N: Unpaired: I DON'T KNOW IF THIS IS
> > CORRECT (cns.unpaired keeps me telling that the reference sample is made
> of
> > 102 files instead of one!).
> > avgN <- getAverageFile(dsN);
>
> This is the correct command and 'avgN' should *indeed* a single file
> ("array") here. You should be able verify by looking at what:
>
> print(avgN);
>
> returns.
>
> > cns.unpaired <- CbsModel(dsT, avgN);
>
> This should work, because 'dsT' is a data set; verify by
>
> print(dsT);
>
> If it doesn't work please let us know what:
>
> print(dsT);
> print(avgN);
>
> returns and what the complete error message is.
>
> > fit(cns.unpaired, verbose=TRUE);
> > regDatList.unpaired <- getRegions(cns.unpaired);
>
> [snip]
>
> I'll answer your second question in a separate thread ...and when I
> find the time.
>
> /Henrik
>
> > Thank you very much for your help!
> > Best,
> > Xavi.
> > #SESSION INFO
> >> sessionInfo()
> > R version 2.13.0 (2011-04-13)
> > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
> > locale:
> > [1] C
> > attached base packages:
> > [1] stats graphics grDevices utils datasets methods base
> > other attached packages:
> > [1] DNAcopy_1.26.0 aroma.cn_0.5.2 aroma.affymetrix_2.1.0
> > [4] aroma.apd_0.1.8 affxparser_1.24.0 R.huge_0.2.2
> > [7] aroma.core_2.1.0 aroma.light_1.20.0 matrixStats_0.2.2
> > [10] R.rsp_0.5.3 R.cache_0.4.2 R.filesets_1.0.1
> > [13] digest_0.5.0 R.utils_1.7.5 R.oo_1.8.0
> > [16] R.methodsS3_1.2.1
> > loaded via a namespace (and not attached):
> > [1] tools_2.13.0
> >
> > --
> > 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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> > 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/
> >
>
> --
> 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
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> To unsubscribe and other options, go to
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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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