[BioC] DEXSeq offset term
Alicia Martin [guest]
guest at bioconductor.org
Tue Oct 9 04:36:33 CEST 2012
I am interested in using DEXSeq to look for differential expression across seven conditions, each with ~7 biological replicates. I have created an ExonCountSet object and am trying to estimate the dispersions from my model. I have two questions: 1) Is it possible to supply an offset term to the glm? This would be very helpful when trying to incorporate normalization info, since the count data is restricted to integers. I noticed that the glmnb.fit object called by DEXSeq contains a mf$offset variable. Additionally, 2) Has anyone seen and/or corrected the following error when trying to use multiple cores to estimate dispersions?
ecs <- estimateDispersions(ecs, nCores=3)
Estimating Cox-Reid exon dispersion estimates using 3 cores. (Progress report: one dot per 100 genes)
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.
This message repeats several times and also contains the following: Tcl_ServiceModeHook: Notifier not initialized.
Thanks a bunch for any potential insight!
-- output of sessionInfo():
R version 2.15.1 (2012-06-22)
Platform: x86_64-apple-darwin12.0.0 (64-bit)
attached base packages:
 splines stats graphics grDevices utils datasets methods
other attached packages:
 DEXSeq_1.2.1 Biobase_2.16.0 BiocGenerics_0.2.0
 RColorBrewer_1.0-5 scales_0.2.2 cqn_1.2.0
 quantreg_4.91 SparseM_0.96 preprocessCore_1.18.0
 nor1mix_1.1-3 mclust_4.0 plyr_1.7.1
loaded via a namespace (and not attached):
 biomaRt_2.12.0 colorspace_1.1-1 dichromat_1.2-4 hwriter_1.3
 labeling_0.1 munsell_0.4 RCurl_1.95-0 statmod_1.4.16
 stringr_0.6.1 tcltk_2.15.1 tools_2.15.1 XML_3.95-0
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