[BioC] rma of oligo feature set crashes R

[Benilton Carvalho]

Can you please try:

pms = pm(affyGeneFS)
apply(!is.finite(pms), 2, table)

(if you see TRUE for any sample, that's not a good sign)

Then compare the file sizes of the files for which you saw TRUE on the
above command... Big divergences on file sizes may indication file
corruption.


b

2013/5/10 Ou, Jianhong <Jianhong.Ou at umassmed.edu>:
> Hi all,
>
> When I do ram of oligo, R crashed. It is very similar to https://stat.ethz.ch/pipermail/bioconductor/2011-October/041567.html. Here is the output of console,
>
>> library(oligo)
>> library(limma)
>> library(pd.hugene.1.0.st.v1)
> Loading required package: RSQLite
> Loading required package: DBI
>> targets<-readTargets(file="filelist.txt",sep=" ",row.names="cel_files")
>> affyGeneFS <- read.celfiles(targets$cel_files)
> Platform design info loaded.
> Reading in : Control-1-1_(HuGene-1_0-st-v1).CEL
> Reading in : CONTROL-1-2-(HuGene-1_0-st-v1).CEL
> Reading in : Control-2-3_(HuGene-1_0-st-v1).CEL
> Reading in : CONTROL-2-4-(HuGene-1_0-st-v1).CEL
> Reading in : Control-3-5_(HuGene-1_0-st-v1).CEL
> Reading in : CONTROL-3-6-(HuGene-1_0-st-v1).CEL
> Reading in : kd-1_7-(HuGene-1_0-st-v1).CEL
> Reading in : KD-1-8_(HuGene-1_0-st-v1).CEL
> Reading in : kd-2_9-(HuGene-1_0-st-v1).CEL
> Reading in : KD-2-10_(HuGene-1_0-st-v1).CEL
> Reading in : kd-3_11-(HuGene-1_0-st-v1).CEL
> Reading in : KD-3-12_(HuGene-1_0-st-v1).CEL
>> sessionInfo()
> R version 3.0.0 (2013-04-03)
> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
> [1] pd.hugene.1.0.st.v1_3.8.0 RSQLite_0.11.3
> [3] DBI_0.2-7                 limma_3.16.3
> [5] oligo_1.24.0              Biobase_2.20.0
> [7] oligoClasses_1.22.0       BiocGenerics_0.6.0
>
> loaded via a namespace (and not attached):
>  [1] affxparser_1.32.0     affyio_1.28.0         BiocInstaller_1.10.1
>  [4] Biostrings_2.28.0     bit_1.1-10            codetools_0.2-8
>  [7] ff_2.2-11             foreach_1.4.0         GenomicRanges_1.12.2
> [10] IRanges_1.18.0        iterators_1.0.6       preprocessCore_1.22.0
> [13] splines_3.0.0         stats4_3.0.0          zlibbioc_1.6.0
>
>> geneCore <- rma(affyGeneFS, target = "core")
> Background correcting
>
>  *** caught segfault ***
> address 0x1029fb000, cause 'memory not mapped'
>
> Traceback:
>  1: .Call("rma_c_complete_copy", pmMat, pnVec, nPn, normalize, background,     bgversion, verbose, PACKAGE = "oligo")
>  2: basicRMA(pms, pnVec, normalize, background)
>  3: .local(object, ...)
>  4: rma(affyGeneFS, target = "core")
>  5: rma(affyGeneFS, target = "core")
>
> Possible actions:
> 1: abort (with core dump, if enabled)
> 2: normal R exit
> 3: exit R without saving workspace
> 4: exit R saving workspace
> Selection: 1
> aborting ...
> Segmentation fault: 11
>
> Any ideas?
>
> Yours sincerely,
>
> Jianhong Ou
>
>         [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor