hi Kevin,

It could be the rows with zero coverage. I have an example of removing rows
with zero coverage in the third code chunk of section 3.5 of the vignette.

Mike



On Mon, Apr 29, 2013 at 9:32 PM, Kevin Lee <kevinjosephlee@gmail.com> wrote:

> 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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