[BioC] DESeq multifactor GLM Error attributed to zero counts (coded as NA) in dataset?
anders at embl.de
Thu Aug 11 17:39:23 CEST 2011
On 08/10/2011 10:35 PM, Steve Vollmer wrote:
> 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.
Occasionally, glm.fit fails to converge and then the function throws an
error. Just yesterday, I've updated DESeq and wrapped the call to
glm.fit in a 'try' statement, so that the function finishes and you just
get a few NAs as p values from these cases.
Let me know if the problem persists in DESeq version 1.5.24.
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