[BioC] Calculate BCV in edgeR - sample without replicates

[Ryan]

Hi Atul,

I believe that all you need to do is to restore the correct grouping 
before calling exactTest, i.e. something like:

norm.tags2$samples$groups = c(1,2)


-Ryan
On Wed Dec 18 13:08:12 2013, Atul Kakrana wrote:
> 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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