Hi.
On Mon, Jun 29, 2009 at 5:14 AM,
cstratowa<christian.strat...@vie.boehringer-ingelheim.com> wrote:
>
> Dear Henrik,
>
> Meanwhile I have downloaded the latest versions from your repository
> and installed them on R-2.8.1. Please note that due to our settings it
> is NOT POSSIBLE for me to use hbInstall("aroma.affymetrix")!!!
>
> Sadly, now CBS does no longer work at all. I get the message:
>
> Loading required package: DNAcopy
> Loading required package: Cairo
> Error: package 'DNAcopy' does not have a name space
> In addition: Warning messages:
> 1: In log(theta/thetaRef, base = 2) : NaNs produced
> 2: In log(theta * thetaRef, base = 2) : NaNs produced
> Execution halted
Output from traceback() would be helpful here. I can make a guess
where/why it occurs, but I'm not sure what you are doing.
>
> Thus it seems that the new versions do not work with R-2.8.1, so I
> need to downgrade to the old versions.
>
> Here is the sessionInfo() for the new versions:
>> 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_0.2.43 RODBC_1.2-5
> aroma.affymetrix_1.1.0
> [4] aroma.apd_0.1.3 R.huge_0.1.7
> affxparser_1.14.2
> [7] aroma.core_1.1.2 aroma.light_1.13.2
> matrixStats_0.1.4
> [10] R.rsp_0.4.0 R.httpd_0.1.1
> R.filesets_0.5.2
> [13] digest_0.3.1 R.cache_0.1.7
> R.utils_1.1.6
> [16] R.oo_1.4.6 R.methodsS3_1.0.3
Version of DNAcopy?
So, I am quite sure the aroma.* code is working on much older
versions, but I cannot speak for external packages.
However, in this case aroma.* do assume that DNAcopy has a namespace
and that was most likely introduced in v1.18.0. You might have to
upgrade DNAcopy to v1.18.0 or newer. I really recommend v 1.19.2
because it is now much much faster (really!). For people who can use
our install scripts, this can be done by fooling bioc to think you
have a newer R version as follows:
source("http://www.braju.com/R/hbLite.R";);
biocLite("DNAcopy", rver="2.10.0");
If you cannot use this, you probably have to download the file
*.tar.gz (*.zip) file and install it manually.
Let us know if this solves the problem.
/Henrik
>
> Best regards
> Christian
>
> P.S.: I know that this is OSS and everybody is very busy, but
> nevertheless I would like to mention, that I am not the only person
> who is not happy with the policy of many open source software systems
> to supply a new version every 6 months and no longer support older
> versions. This is no problem when running the software on one's
> personal PC but often causes problems in company settings where you
> need to upgrade a lot of systems and the philosophy is not to change a
> running system. In our case this means to update the servers and the
> Linux clusters, too, since I have created a package which allows me to
> run CBS and GLAD on the cluster nodes.
>
>
> On Jun 26, 7:35 am, Henrik Bengtsson <h...@stat.berkeley.edu> wrote:
>> 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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