[BioC] multicore and DEXSeq

[Lynn Amon]

I just tried library(parallel) and now it does estimateDispersions does
recognize my cores.
Lynn

On 7/30/12 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),"/h
>>tseq_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...
>
>
>
> -- 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.