Hello Gentlepeople,

I have been using the edgeR package to identify differentially abundant
tags in an RNA-seq experiment.

I was happy when the edgeR package version 2.4.6 called 41 differentially
abundant tags.

However, now I am unhappy because the same analysis with edgeR package
version 3.0.2 does not call any differentially abundant tags.

I've compared the output of the two versions and I can see that both 
versions
calculate the same fold changes - however - the p-value calculation is 
different.

I feel that the optimal solution for me is to determine the command 
arguments
that I can use to emulate the previous default behavior.

Can anyone help me figure that out?
I would be extremely grateful for some guidance.
This way, I could keep my bioconductor packages up to date.

If you think you can help then please see below, for the code and 
session Info.

Thank you for your time.

sincerely,
Lee Brooks

----
HERE IS THE CODE PART

Here is the procedure that I have been using,
where x is the data frame object containing my data:
y <- DGEList(counts=x,group=group)
y <- calcNormFactors(y)
y <- estimateCommonDisp(y)
y <- estimateTagwiseDisp(y)
et <- exactTest(y)
topTags(et)
de <- decideTestsDGE(et, p=0.05, adjust="BH")
detags <- et[as.logical(de)]
detags <- topTags(detags, n = length(detags))

----
HERE IS AN EXAMPLE OUTPUT FROM EACH VERSION:

Tables Tables

	logFC 	logCPM 	PValue 	FDR
fooTag_edgeR_2.4.6 	5.12318 	12.6577 	2.9E-30 	8.9E-26
fooTag_edgeR_3.0.2 	5.12318 	12.6612 	0.00717 	1


-----
HERE IS THE sessionInfo() PART...

THE CONFIGURATION THAT WORKED FOR ME:

R version 2.14.1 (2011-12-22)
Platform: i686-pc-linux-gnu (32-bit)

locale:
  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
  [7] LC_PAPER=C                 LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
[1] edgeR_2.4.6  limma_3.10.3

THE CONFIGURATION THAT DOES NOT WORK FOR ME:

R version 2.15.2 (2012-10-26)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
  [1] LC_CTYPE=en_US.utf8       LC_NUMERIC=C
  [3] LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8
  [5] LC_MONETARY=en_US.utf8    LC_MESSAGES=en_US.utf8
  [7] LC_PAPER=C                LC_NAME=C
  [9] LC_ADDRESS=C              LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C

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

other attached packages:
[1] edgeR_3.0.2  limma_3.14.1



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