Dear Henrik,
Sadly, paired analysis with SNP6.0 arrays results still in the Error
messages shown below.
Please note the following:
1, With the new versions of aroma.* I have just successfully tested
CEL-files from Mapping250K_Sty arrays both with and w/o paired
analysis.
2, As mentioned yesterday I have successfully tested CEL-files from
SNP6.0 arrays w/o paired analysis.
3, Since the error seems to occur in function "computeCN()" please
note that I have already listed the relevant code in my initial
message.
Here is the error message I get:
Loading required package: DNAcopy
Error in list(`computeCN(aroma, model = model, arrays = arrays[i],
chromosomes = 1:23, ref` = <environment>, :
[2009-07-02 10:21:14] Exception: Range of argument 'idx' is out of
range [1,0]: [1,1]
at throw(Exception(...))
at throw.default(sprintf("Range of argument '%s' is out of range [%s,
%s]: [%s,
at throw(sprintf("Range of argument '%s' is out of range [%s,%s]:
[%s,%s]", .n
at getNumerics.Arguments(static, ..., asMode = "integer", disallow =
disallow)
at getNumerics(static, ..., asMode = "integer", disallow = disallow)
at getIntegers.Arguments(static, ..., range = range)
at getIntegers(static, ..., range = range)
at getIndices.Arguments(static, ..., length = length)
at getIndices(static, ..., length = length)
at method(static, ...)
at Arguments$getIndex(idx, range = c(1, nbrOfFiles(this)))
at getFile.GenericDataFileSet(this, 1)
at getFile(this, 1)
at getUnitNamesFile.AffymetrixCelSet(this)
at getUnitNamesFile(this)
at getChipType.AffymetrixCelSet(X[[1]], ...)
at FUN(X[[1]], ...)
at lapply(X, FUN, ...)
at sapply.default(csList, FUN = getChipTyp
Calls: computeCN ... getNumerics.Arguments -> throw -> throw.default -
> throw -> throw.Exception
Execution halted
Do you have any idea what might be the reason?
Since I do not get this error with Sty arrays it must be special for
SNP6.0 arrays when doing paired analysis. Could it be that there may
be a problem with aroma functions "getNames()" or "extract()" for
SNP6.0?
Here once again the 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] GLAD_1.18.0 Cairo_1.4-5
DNAcopy_1.19.2
[4] biasnp_0.2.43 RODBC_1.2-5
aroma.affymetrix_1.1.0
[7] aroma.apd_0.1.3 R.huge_0.1.7
affxparser_1.14.2
[10] aroma.core_1.1.2 aroma.light_1.13.2
matrixStats_0.1.6
[13] R.rsp_0.4.0 R.httpd_0.1.1
R.filesets_0.5.2
[16] digest_0.3.1 R.cache_0.1.7
R.utils_1.1.6
[19] R.oo_1.4.6 R.methodsS3_1.0.3
Best regards
Christian
On Jul 1, 3:31 pm, cstratowa <christian.strat...@vie.boehringer-
ingelheim.com> wrote:
> Dear Henrik,
>
> Thank you for your suggestions.
>
> The answer to your first reply is that the security settings prevent
> us from using biocLite() etc so we need to download all files and
> usually run install scripts.
>
> Following your suggestion I have now installed DNAcopy v 1.19.2 which
> caused some problems on the cluster because of a missing
> libgfortran.so. (As I have mentioned in an earlier post, I am running
> CBS and GLAD on cluster nodes in order to speed up processing.)
>
> I have just started another session and at the moment it seems to
> work, the current output is:
>
> Loading required package: DNAcopy
> Loading required package: Cairo
> Loading required package: GLAD
> [1] "Have fun with GLAD"
>
> However, I still need to test the paired analysis with the SNP6.0
> arrays, this will take some time.
>
> Here is how the sessionInfo is supposed to look like:> 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] GLAD_1.18.0 Cairo_1.4-5
> DNAcopy_1.19.2
> [4] biasnp_0.2.43 RODBC_1.2-5
> aroma.affymetrix_1.1.0
> [7] aroma.apd_0.1.3 R.huge_0.1.7
> affxparser_1.14.2
> [10] aroma.core_1.1.2 aroma.light_1.13.2
> matrixStats_0.1.6
> [13] R.rsp_0.4.0 R.httpd_0.1.1
> R.filesets_0.5.2
> [16] digest_0.3.1 R.cache_0.1.7
> R.utils_1.1.6
> [19] R.oo_1.4.6 R.methodsS3_1.0.3
>
> Best regards
> Christian
>
> On Jun 29, 4:34 pm, Henrik Bengtsson <h...@stat.berkeley.edu> wrote:
>
> > 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
>
> ...
>
> read more »
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