[BioC] rma of oligo feature set crashes R

[Benilton Carvalho]

You'll need to either find non-damaged copies of these files or remove
them from analysis. b

2013/5/13 Ou, Jianhong <Jianhong.Ou at umassmed.edu>:
> 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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