Dear listers,


I get the following error message in the new (beta) version of DESeq when I
try to implement the fitNbinomGLMs function [e.g.fitNbinomGLMs(cds, count ~
treatment + condition)].

Error in glm.fit(x = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0,  :
  NA/NaN/Inf in foreign function call (arg 1)


This error message occurs regardless of which method (pooled, blind,
etc.) that I use to estimateDispersions.


It seemed likely that the problem was due to NAs coded into the cds
during the dispersion estimates, so I used a subset of the data where
at least one count was observed in every sample for each gene
transcript (this is RNAseq data). THEN, the error goes away.


Has anyone figured out a sensible workaround to this problem?


Cheers,

Steve

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