Alicia Martin [guest] | 9 Oct 04:36 2012

DEXSeq offset term

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 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
to debug.

This message repeats several times and also contains the following: Tcl_ServiceModeHook: Notifier not

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)

[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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