On Fri, Jun 17, 2011 at 12:15 PM, Henrik Bengtsson
<henrik.bengts...@aroma-project.org> wrote:
> 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);
I forgot to add that you should find the recent thread 'Combine paired
and unpaired CN analysis' (started on May 23, 2001) useful:
https://groups.google.com/forum/#!topic/aroma-affymetrix/220dWcCxxn8
/Henrik
>
> [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.
>>
>>
>> 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/
>>
>
--
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/
