Hi All,

I am working on sRNA-seq data and with no replicates and using edgeR to
identify differentially expressed tags and using an arbitrary BCV value
(0.3) based on suggestion in edgeR manual:

"Simply pick a reasonable dispersion value, based on your experience
with similar data, and use that for exactTest or glmFit. Typical values
for the common BCV (square- root-dispersion) for datasets arising from
well-controlled experiments are 0.4 for human data, 0.1 for data on
genetically identical model organisms or 0.01 for technical replicates. "

But I came across this post which mentions a conservative way to
calculate BCV:
[BioC] EdgeR: general advice on using edgeR for sRNA analysis:
https://stat.ethz.ch/pipermail/bioconductor/2013-August/054239.html

I am getting an error calculating BCV using the approach discussed in
post. Here is my code

norm.tags2 <- norm.tags
norm.tags2$samples$groups = c(1,1)
norm.tags2 <- estimateDisp(norm.tags2,robust=TRUE,winsor.tail=c(0.05,0.2))
results = exactTest(norm.tags,dispersion=norm.tags2$trended.dispersion)

Error in exactTest(norm.tags, dispersion = norm.tags2$trended.dispersion) :
  At least one element of given pair is not a group.
 Groups are:

I believe the error is because I have grouped samples as replicates for
calculating BCV while they are being compared against each other in
exactTest. Can I calculate the dispersion values from samples? rather
than setting arbitrarily?

I would really appreciate any help. Awaiting reply.

Atul





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