[BioC] multicore and DEXSeq

[Lynn Amon]

Actually, I'm still running into problems with the parallel package.  Here is my error with estimateDispersions:

> glueExons <- estimateDispersions(glueExons,nCores=4)
Estimating Cox-Reid exon dispersion estimates using 4 cores. (Progress report: one dot per 100 genes)
Error in function (classes, fdef, mtable)  :
  unable to find an inherited method for function "fData", for signature "character"
In addition: Warning message:
In parallel::mclapply(allecs, FUN = funtoapply, mc.cores = mc.cores) :
  all scheduled cores encountered errors in user code


________________________________________
From: Dan Tenenbaum [dtenenba at fhcrc.org]
Sent: Monday, July 30, 2012 1:02 PM
To: Lynn Amon
Cc: Lynn Amon [guest]; bioconductor at r-project.org; DEXSeq Maintainer
Subject: Re: [BioC] multicore and DEXSeq

On Mon, Jul 30, 2012 at 12:59 PM, Lynn Amon <lynn.amon at seattlebiomed.org> wrote:
> Dan,
> Thanks for the reply.  library(parallel) does work.  I used multicore
> because that what vignette for DEXSeq uses.

Thanks for the clarification. The DEXSeq vignette should be
updated...Alejandro, would you mind doing that?

Thanks,
Dan


> 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
>>>
>>>
>>> --
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>>>
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>