[BioC] rma of oligo feature set crashes R

[Ou, Jianhong]

Dear Benilton,

Yes, I found two files contain TRUE (485 and 138). However the file sizes
are similar to the others. I will double check the md5 checksums.
Thank you for your help.

Yours sincerely,

Jianhong Ou

LRB 670A
Program in Gene Function and Expression
364 Plantation Street Worcester,
MA 01605




On 5/12/13 6:02 PM, "Benilton Carvalho" <beniltoncarvalho at gmail.com> wrote:

>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]]
>>
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