Hi Steve, 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. Simon