Hi Iain,
Can you send me a reproducible example, plus the output of sessionInfo() and
traceback() after the error, please? It'll probably be too large for email, so
maybe use Dropbox or dropsend ..
My guess is that the units with >500 probes actually have NAs. Maybe you can
check this also beforehand?
Best, Mark
On 04.06.2015, at 16:07, Iain <iaingallag...@gmail.com> wrote:
> Hi
>
> We're trying to calculate the difference in residuals between two groups and
> generate mufScores (FIRMAGene) on those residual differences. Calculating the
> differences goes smoothly:
>
> rsu_diff <- lapply(unlist(rsu, use.names=FALSE), byrow=FALSE,
> ncol=length(unique(cls)))
>
> where cls is a grouping variable (e.g. cls <- c('A', 'A, 'B', 'B')
>
> Next we apply the mufColumns function to the elements of the rsu_diff object.
>
> mufScores <- lapply(rsu_diff[w], FUN = function(u), c(mufColumns(u)))
>
> w is an indicator variable that only keeps genes (this is gene level
> analysis) if the gene has more than 3 probes and less than some other number.
> If we set the upper limit of w to >500 we get the following error.
>
> Error in mufC(x): Nan/NA/Inf in foreign function call
>
> Having looked at the C code for the relevant function (mps.c) I can only see
> one line where that could cause this:
>
> x[count]=sum/sqrt(j-i+1.);
>
> Can anyone shed any light on why we can't run mufColumns if we select genes
> with more than 500 probes over the gene?
>
> Thanks,
>
> Iain
>
>
>
>
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----------
Prof. Dr. Mark Robinson
Statistical Bioinformatics Group, UZH
http://ow.ly/riRea
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