2009/6/22 cstratowa <christian.strat...@vie.boehringer-ingelheim.com>:
>
> Does this update also work with R-2.8.1?
I avoid increasing the dependency in the DESCRIPTION files unless I
know they have to. Currently I think it is roughly R 2.6.x that is
specified. It does not mean it is guaranteed to work. However, I
only support and run redundancy tests on the lastest stable version of
R (now R 2.9.x).
Did you try?
/Henrik
>
> Best regards
> Christian
>
> On Jun 18, 5:39 pm, Henrik Bengtsson <h...@stat.berkeley.edu> wrote:
>> Hi,
>>
>> update aroma.affymetrix et al. and retry.
>>
>> /Henrik
>>
>> On Thu, Jun 18, 2009 at 5:01 AM,
>>
>> cstratowa<christian.strat...@vie.boehringer-ingelheim.com> wrote:
>>
>> > Dear all,
>>
>> > Below I show you the relevant code fragments of my function "computeCN
>> > ()" to compute copy-number regions using model CBS. This function can
>> > compute copy-number regions for the usual case (reference=NULL), for
>> > pairs of samples (reference="Pairs") or using reference samples
>> > (reference="Reference").
>>
>> > I am using this function for a long time for 100K and 500K mapping
>> > arrays w/o any problems. However for the SNP6.0 array this function
>> > works only for the usual case (reference=NULL), but not for the Pairs/
>> > Reference cases.
>>
>> > For SNP6.0 array and Pairs/Reference cases I get always the following
>> > error message:
>>
>> > Error in this$files[[1]] : subscript out of bounds
>> > Calls: computeCN ... clearCache.AffymetrixCelSet -> getCdf ->
>> > getCdf.AffymetrixCelSet -> getCdf
>> > Execution halted
>>
>> > Do you have any idea why I get these errors?
>> > Do I have to change the code for Pairs/Reference cases, and how?
>>
>> > Here is the relevant code of function "computeCN()":
>>
>> > "computeCN" <- function(object, pheno, arrays=NULL, reference=NULL,
>> > chromosomes=NULL) {
>> > ## get normalized data
>> > cesList <- effectSet(object);
>>
>> > ## get optional reference set
>> > if (is.null(reference)) {
>> > refList <- NULL;
>> > } else if (is.character(reference)) {
>> > ## extract reference samples (and data samples if paired)
>> > refList <- list();
>> > for (chiptype in names(cesList)) {
>> > ces <- cesList[[chiptype]];
>> > cesnames <- getNames(ces);
>>
>> > ## get row numbers containing reference and data samples
>> > refcol <- which(pheno[,reference] == 1);
>> > datcol <- which(pheno[,reference] == 0);
>>
>> > if (reference == "Pairs") {
>> > cesList[[chiptype]] <- extract(ces, datcol);
>> > refList[[chiptype]] <- extract(ces, refcol);
>> > } else if (reference == "Reference") {
>> > cesRef <- extract(ces, refcol);
>> > ceRef <- getAverageFile(cesRef);
>>
>> > ## convert single ceRef file into a set of identical files
>> > of same size/length as ces
>> > numarr <- nbrOfArrays(ces);
>> > cesRef <- rep(list(ceRef), numarr); # becomes a list of
>> > CnChipEffectFile:s
>> > cesRef <- newInstance(ces, cesRef, mergeStrands=ces
>> > $mergeStrands, combineAlleles=ces$combineAlleles);
>> > refList[[chiptype]] <- cesRef;
>> > }#if
>> > }#for
>> > }#if
>>
>> > ## select model
>> > model <- CbsModel(cesList, refList);
>>
>> > ## get index of arrays
>> > if (is.null(arrays)) {
>> > arrays <- indexOfArrays(model);
>> > } else {
>> > arrays <- which(getNames(model)==arrays);
>> > }#if
>>
>> > ## fit model with Chromosome Explorer
>> > ce <- ChromosomeExplorer(model, tags=tags);
>> > setParallelSafe(ce, status=TRUE); #necessary for running on cluster
>> > tmp <- process(ce, arrays=arrays, chromosomes=chromosomes,
>> > force=force, verbose=verbose);
>>
>> > ## get fitted CN regions from model
>> > cnrs <- getRegions(model, arrays=arrays, chromosomes=chromosomes,
>> > organism="Human", hgVersion="hg18");
>>
>> > return(object);
>> > }#computeCN
>>
>> > Here is my sessionInfo:
>>
>> >> sessionInfo()
>> > R version 2.8.1 (2008-12-22)
>> > x86_64-unknown-linux-gnu
>>
>> > locale:
>> > C
>>
>> > attached base packages:
>> > [1] tcltk stats graphics grDevices utils datasets
>> > methods
>> > [8] base
>>
>> > other attached packages:
>> > [1] biasnp_0.2.41 RODBC_1.2-5
>> > aroma.affymetrix_1.0.1
>> > [4] aroma.apd_0.1.3 R.huge_0.1.6
>> > affxparser_1.14.2
>> > [7] aroma.core_1.0.1 aroma.light_1.11.1
>> > digest_0.3.1
>> > [10] matrixStats_0.1.4 R.rsp_0.4.0
>> > R.httpd_0.1.1
>> > [13] R.cache_0.1.7 R.utils_1.1.3
>> > R.oo_1.4.6
>> > [16] R.methodsS3_1.0.3
>>
>> > Thank you in advance for your help.
>>
>> > Best regards
>> > Christian
> >
>
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