Does this update also work with R-2.8.1?
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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