[BioC] DEXSeq offset term

[Alicia Martin [guest]]

Hi all,

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(): 

> sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-apple-darwin12.0.0 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] splines   stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
 [1] DEXSeq_1.2.1          Biobase_2.16.0        BiocGenerics_0.2.0   
 [4] RColorBrewer_1.0-5    scales_0.2.2          cqn_1.2.0            
 [7] quantreg_4.91         SparseM_0.96          preprocessCore_1.18.0
[10] nor1mix_1.1-3         mclust_4.0            plyr_1.7.1           
[13] multicore_0.1-7      

loaded via a namespace (and not attached):
 [1] biomaRt_2.12.0   colorspace_1.1-1 dichromat_1.2-4  hwriter_1.3     
 [5] labeling_0.1     munsell_0.4      RCurl_1.95-0     statmod_1.4.16  
 [9] stringr_0.6.1    tcltk_2.15.1     tools_2.15.1     XML_3.95-0      

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