[BioC] edgeR, glmLRT error

[Cei Abreu-Goodger]

Hi Gordon,

I've been getting the following error upon running glmLRT:

Error in beta[k, ] <- betaj[decr, ]
   NAs are not allowed in subscripted assignments

which has previously been reported, for instance:

https://stat.ethz.ch/pipermail/bioconductor/2011-February/038079.html

I subsetted my count data (originally ~14k rows) to narrow down the 
culprit row, and I would like to send you this example in case it can be 
used to improve the glm fitting code. If it turns out to be impossible 
to completely avoid these kinds of errors, perhaps it would be nice to 
return the genes that are generating the NAs so that we can more easily 
remove them and proceed?

I can also avoid this particular case by using only the CommonDisp or 
heavily increasing the prior.n, but that kind of defeats the purpose of 
the TagwiseDisp.

Example code and sessionInfo:

################
library(edgeR)

counts <- read.table("http://datos.langebio.cinvestav.mx/~cei/counts.tab")
grp <- sub("_R.+", "", colnames(counts))
dge <- DGEList(counts=counts, group=grp)
dge <- calcNormFactors(dge)

design <- model.matrix(~0 + dge$samples$group)
colnames(design) <- levels(dge$samples$group)

dge <- estimateGLMCommonDisp(dge, design)
dge <- estimateGLMTagwiseDisp(dge, design)

fit <- glmFit(dge, design)
lrt <- glmLRT(dge, fit, contrast=c(0,0,0,-1,0.5,0.5))

Error in beta[k, ] <- betaj[decr, ] :
   NAs are not allowed in subscripted assignments

################
R version 2.15.0 (2012-03-30)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

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

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

other attached packages:
[1] edgeR_2.6.9         limma_3.12.1        Biobase_2.16.0 
BiocGenerics_0.2.0  BiocInstaller_1.4.7

################


Many thanks,

Cei

-- 
Dr. Cei Abreu-Goodger
Langebio CINVESTAV
Tel: (52) 462 166 3006
cei at langebio.cinvestav.mx


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