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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>
--
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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