[BioC] parallel and GSVA
David Iles
D.E.Iles at leeds.ac.uk
Sat Jan 12 11:47:18 CET 2013
Hi Robert,
You appear to be correct in your assumption that there may be an issue with the GSVA package running in the R64.app GUI on a Mac. Following Steve's suggestion, the following went smoothly running R from Terminal:
> leukemia_es <- gsva(leukemia_filtered_eset, c2BroadSets,min.sz=10, max.sz=500, verbose=TRUE)$es.obs
Mapping identifiers between gene sets and feature names
Estimating GSVA scores for 2033 gene sets.
Computing observed enrichment scores
Estimating ECDFs in microarray data with Gaussian kernels
Using parallel with 8 cores
|======================================================================| 100%
>
Thanks for your help.
Dave
Dr David Iles
School of Biology
University of Leeds
Leeds LS2 9JT
d.e.iles at leeds.ac.uk
> sessionInfo()
R version 2.15.2 (2012-10-26)
Platform: i386-apple-darwin9.8.0/i386 (32-bit)
locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
attached base packages:
[1] grid stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] Rgraphviz_2.2.1 RBGL_1.34.0 RColorBrewer_1.0-5
[4] limma_3.14.3 genefilter_1.40.0 GSVAdata_0.99.9
[7] hgu95a.db_2.8.0 org.Hs.eg.db_2.8.0 RSQLite_0.11.2
[10] DBI_0.2-5 GSVA_1.6.1 GSEABase_1.20.1
[13] graph_1.36.1 annotate_1.36.0 AnnotationDbi_1.20.3
[16] Biobase_2.18.0 BiocGenerics_0.4.0
loaded via a namespace (and not attached):
[1] Heatplus_2.4.0 IRanges_1.16.4 parallel_2.15.2 splines_2.15.2
[5] stats4_2.15.2 survival_2.37-2 tools_2.15.2 XML_3.95-0.1
[9] xtable_1.7-0
>
On 11 Jan 2013, at 14:29, Robert Castelo <robert.castelo at upf.edu> wrote:
> hi David,
>
> ok, then it's an issue with the parallel package in this platform. you
> can put parallel.sz=8 but that should be in fact the default behavior
> raising the error. GSVA was trying to use all your processors by default
> and that caused the error.
>
> i work usually on linux and therefore i'd need some time to investigate
> this issue in mac, maybe you can try Steve's suggestion to work on the
> terminal window of mac? does it work that way?
>
> robert.
>
> On 01/11/2013 02:26 PM, David Iles wrote:
>> Hi Robert,
>>
>> Thanks for your prompt response.
>>
>> Yes, setting parallel.sz=1 does work. Thanks for that. I have 8 cores available, so can I set parallel.sz=8?
>>
>> Thanks
>>
>> Dave
>>
>> Dr David Iles
>> School of Biology
>> University of Leeds
>> Leeds LS2 9JT
>>
>> d.e.iles at leeds.ac.uk
>>
>>
>>
>>
>>
>> On 11 Jan 2013, at 13:11, Robert Castelo<robert.castelo at upf.edu> wrote:
>>
>>> Dear David,
>>>
>>> just to discard any other issue not related to the parallel execution in
>>> your system, could you try to call the gsva() function adding the
>>> argument parallel.sz=1? does it work?
>>>
>>> cheers,
>>> robert.
>>>
>>> On 01/11/2013 01:18 PM, David Iles wrote:
>>>> Hi Folks,
>>>>
>>>> I want to run a GSVA analysis on a set of Affymetrix hgu133plus2 arrays. To familiarise myself with the GSVA code, I worked through the example in the vignette, but encountered the following issue...
>>>>
>>>>> data(leukemia)
>>>>> data(c2BroadSets)
>>>>> library(parallel)
>>>>> filtered_eset<- nsFilter(leukemia_eset, require.entrez=TRUE, remove.dupEntrez=TRUE,
>>>> + var.func=IQR, var.filter=TRUE, var.cutoff=0.5, filterByQuantile=TRUE,
>>>> + feature.exclude="^AFFX")
>>>>> leukemia_filtered_eset<- filtered_eset$eset
>>>>> leukemia_es<- gsva(leukemia_filtered_eset, c2BroadSets, min.sz=10, max.sz=500, verbose=TRUE)$es.obs
>>>> Mapping identifiers between gene sets and feature names
>>>> | | 0%)
>>>>
>>>> The process has forked and you cannot use this CoreFoundation functionality safely. You MUST exec().
>>>> Break on __THE_PROCESS_HAS_FORKED_AND_YOU_CANNOT_USE_THIS_COREFOUNDATION_FUNCTIONALITY___YOU_MUST_EXEC__() to debug.
>>>>
>>>> ....etcetcetc. The process hangs here.
>>>>
>>>> I get the same messages with my own data. I must have overlooked something. Any suggestions?
>>>>
>>>> Dr David Iles
>>>> School of Biology
>>>> University of Leeds
>>>> Leeds LS2 9JT
>>>>
>>>> d.e.iles at leeds.ac.uk<mailto:d.e.iles at leeds.ac.uk>
>>>>
>>>>> sessionInfo()
>>>> R version 2.15.2 (2012-10-26)
>>>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>>>>
>>>> locale:
>>>> [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
>>>>
>>>> attached base packages:
>>>> [1] parallel grid stats graphics grDevices utils datasets methods base
>>>>
>>>> other attached packages:
>>>> [1] RBGL_1.34.0 BiocInstaller_1.8.3 GSVAdata_0.99.9 hgu95a.db_2.8.0 org.Hs.eg.db_2.8.0
>>>> [6] RSQLite_0.11.2 DBI_0.2-5 GSVA_1.6.1 GSEABase_1.20.1 annotate_1.36.0
>>>> [11] AnnotationDbi_1.20.3 Rgraphviz_2.2.1 graph_1.36.1 RColorBrewer_1.0-5 limma_3.14.3
>>>> [16] genefilter_1.40.0 Biobase_2.18.0 BiocGenerics_0.4.0
>>>>
>>>> loaded via a namespace (and not attached):
>>>> [1] IRanges_1.16.4 splines_2.15.2 stats4_2.15.2 survival_2.37-2 tools_2.15.2 XML_3.95-0.1 xtable_1.7-0
>>>>
>>>> _______________________________________________
>>>> 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
>>>>
>>>
>>> --
>>> Robert Castelo, PhD
>>> Associate Professor
>>> Dept. of Experimental and Health Sciences
>>> Universitat Pompeu Fabra (UPF)
>>> Barcelona Biomedical Research Park (PRBB)
>>> Dr Aiguader 88
>>> E-08003 Barcelona, Spain
>>> telf: +34.933.160.514
>>> fax: +34.933.160.550
>>>
>>> _______________________________________________
>>> 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
>>
>>
>
> --
> Robert Castelo, PhD
> Associate Professor
> Dept. of Experimental and Health Sciences
> Universitat Pompeu Fabra (UPF)
> Barcelona Biomedical Research Park (PRBB)
> Dr Aiguader 88
> E-08003 Barcelona, Spain
> telf: +34.933.160.514
> fax: +34.933.160.550
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