Hello,

I am working with ExomeCopy, and I cannot get past this error:

fit.list <- lapply(sample.names, runExomeCopy, seqs)
*Error in negLogLike(c(logit(goto.cnv), logit(goto.normal), beta.hat,
log(phi.hat)),  :*
*  NA/NaN/Inf in foreign function call (arg 5)*

where:
runExomeCopy <- function(sample.name, seqs) { lapply(seqs, function(seq.name)
exomeCopy(counts[seq.name], sample.name, X.names = c("log.bg", "GC",
"GC.sq", "width"), S = 0:4, d = 2)) }

(I have followed the vignette as closely as possible.)


There are some exons that have zero reads for all 7 samples.  Could this be
causing the error?  And if so, how can I remove these rows (ranges) from
the counts RangeData object?


Cheers,

Kevin


-- 
Kevin Lee
Georgia Institute of Technology
Department of Biology
PhD candidate in Bioinformatics

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