[BioC] multicore and DEXSeq

[Dan Tenenbaum]

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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