[BioC] multicore and DEXSeq

[Lynn Amon]

Dan,
Thanks for the reply.  library(parallel) does work.  I used multicore
because that what vignette for DEXSeq uses.
Lynn

On 7/30/12 12:55 PM, "Dan Tenenbaum" <dtenenba at fhcrc.org> wrote:

>Hi Lynn,
>
>On Mon, Jul 30, 2012 at 12:51 PM, Lynn Amon [guest]
><guest at bioconductor.org> wrote:
>>
>> Hi,
>> I am having trouble getting fitDespersions to recognize that I have
>>multicore installed. I get an error from divideWork telling me to load
>>parallel package but I have multicore and it detects 8 cores.  Here is
>>some of my script to make an exonCountSet object and then estimate
>>dispersions using four cores.
>> Thanks,
>> Lynn
>>
>>> glueExons <- 
>>>read.HTSeqCounts(countfiles=file.path(bamPath,paste(rownames(samples),"/
>>>htseq_exons.txt",sep="")),design=samples,flattenedfile=annotationFile)
>>>
>>> sampleNames(glueExons) <- rownames(samples)
>>>
>>> expdata <- new("MIAME",name="GlueGenomics")
>>> experimentData(glueExons) <- expdata
>>>
>>> library(DESeq)
>>> genetable <- geneCountTable(glueExons)
>>> glue_genes <- newCountDataSet(genetable,conditions=samples)
>>> experimentData(glue_genes) <- expdata
>>>
>>> glueExons <- estimateSizeFactors(glueExons)
>>> sizeFactors(glueExons)
>>     WT_RY_0_12A    WT_RY_P3_12A   WT_RY_PIC_12A    WT_RY_PP_12A
>>IL10_RZ_0_12A
>>       1.0143924       0.8163463       1.2448730       0.4565408
>>2.7520441
>>  IL10_RY_P3_12A IL10_RY_PIC_12A  IL10_RY_PP_12A
>>       1.1597040       0.8003611       0.9501160
>>>
>>> library(multicore)
>>> multicore:::detectCores()
>> [1] 8
>>> glueExons <- estimateDispersions(glueExons,nCores=4)
>> Estimating Cox-Reid exon dispersion estimates using 4 cores. (Progress
>>report: one dot per 100 genes)
>> Error in divideWork(cds, funtoapply = toapply, fattr =
>>"dispBeforeSharing",  :
>>   Please load first parallel package or set parameter nCores to 1...
>>
>>
>
>Load the "parallel" package, not the "multicore" package.
>Dan
>
>
>
>>
>>  -- output of sessionInfo():
>>
>> R version 2.15.0 (2012-03-30)
>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>
>> locale:
>>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>>  [7] LC_PAPER=C                 LC_NAME=C
>>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>> [1] DESeq_1.9.10       lattice_0.20-6     locfit_1.5-8
>>DEXSeq_1.3.14
>> [5] Biobase_2.17.6     BiocGenerics_0.3.0 multicore_0.1-7
>>
>> loaded via a namespace (and not attached):
>>  [1] annotate_1.35.3       AnnotationDbi_1.19.28 biomaRt_2.13.2
>>  [4] DBI_0.2-5             genefilter_1.39.0     geneplotter_1.35.0
>>  [7] grid_2.15.0           hwriter_1.3           IRanges_1.15.24
>> [10] plyr_1.7.1            RColorBrewer_1.0-5    RCurl_1.91-1
>> [13] RSQLite_0.11.1        splines_2.15.0        statmod_1.4.14
>> [16] stats4_2.15.0         stringr_0.6.1         survival_2.36-14
>> [19] XML_3.9-4             xtable_1.7-0
>>
>>
>> --
>> Sent via the guest posting facility at bioconductor.org.
>>
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