Greetings,

I have been doing some RNA analysis with the limma package using the eBayes
function.  I have a matrix of counts consisting of 25322 genes and 23
samples.  I intended to use the voom function to normalize my data.  Here
is my code and problem:

design <- model.matrix(~factor(class))
colnames(test) <- c("Fasted", "Prefed")

nf = calcNormFactors(sub, method = "TMM")
voom.data <- voom(sub, design = design,
                  lib.size = colSums(sub) * nf)
voom.data$genes = rownames(sub)
voom.fitlimma = lmFit(voom.data, design = design)
voom.fitbayes = eBayes(voom.fitlimma)

Warning message:In ebayes(fit = fit, proportion = proportion,
stdev.coef.lim = stdev.coef.lim,  :
  Estimation of var.prior failed - set to default value


I tried looking into the error and couldn't find a clear answer in the
archives (but I may have missed it).  What I gather is one of the estimated
parameters couldn't be and a default was entered instead.  I don't think I
should just fall on a default when there seems to be something that should
be solvable.  Curious I decided to do subsets of my data and the analysis
would run up to 23800 rows but not 23801 and up.  I then tried to use rows
10000:25322 and that works perfectly!?!?

Is there some sort of limit on rows for eBayes?  - I highly doubt it but I
need to ask given what I am running into.

Any thoughts would be sincerely appreciated as I am vexed by this.

Thanks for your time,
Sincerely,
-- 
Charles Determan
Integrated Biosciences PhD Student
University of Minnesota

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