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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