Hello,
I'm trying to use edgeR to analyze some RNA-seq time series data. I have
four time points. The first and last time points have three replicates,
while the middle two have two replicates. The following gives the error I
get:

require(edgeR)
counts <- read.csv("http://www.duke.edu/~csm29/counts.csv",row.names=1)
d <- DGEList(counts)
d <- calcNormFactors(d)
d <- d[rowSums(d$counts)>9,]
times <- rep(c("zero","one","three","six"),c(3,2,2,3))
design <- model.matrix(~factor(times))
d <- estimateCRDisp(d, design)

Error in beta[k, ] <- betaj[decr, ] :
 NAs are not allowed in subscripted assignments

traceback()
3: mglmLS(y, design, dispersion, offset = offset)
2: adjustedProfileLik(spline.disp[i], y.filt, design = design, offset =
offset.mat.filt +
      lib.size.mat.filt)
1: estimateCRDisp(d, design)

sessionInfo()
R version 2.12.0 (2010-10-15)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] edgeR_2.0.3

loaded via a namespace (and not attached):
[1] limma_3.6.9

The function seems to be getting hung up on one or two genes when I recover
the error. However, when I remove those genes from the data, the problem is
still there. Any help would be much appreciated!

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