Hello,
I have used edgeR for DGE analysis and I have few questions regarding the
model and comparisions.

1) What kind of statistical model is taken into account to analyze treatment
structure and conduct analysis of variance?
2) How does the edgeR correct the multiple comparisions?
3) I am assuming that the calculated  p-values in the output after
performing the tagwiseDispersion are after adjusting for multiple testing.
Please correct me if I am wrong? If so, what kind of multiple testing is
taken into account?

The arguments that I passed are as follows:
>raw.data <- read.delim("c33_con3.txt")
>raw.data.2a <- read.delim ("2c33_con3.txt")
>d2a <- raw.data.2a[, 2:5]
>rownames(d2a) <- raw.data.2a[,1]
>group2a <- c(rep("c33", 2), rep("con3", 2))
>d2a <- DGEList(counts = d2a, group = group2a)
>d2a <- estimateCommonDisp(d2a)
>d2a <- estimateTagwiseDisp(d2a, prior.n = 10, grid.length = 500)
>prior.n2a <- estimateSmoothing(d2a)
>de2a.tgw <- exactTest(d2a, common.disp = FALSE)
> de2a.tgw
An object of class "DGEExact"
$table

logConc       logFC   p.value
MGG_00005 | Mo hypothetical protein (1014 nt)
-16.67772  0.05248378 0.9394668
MGG_00015 | Mo catechol O-methyltransferase (1102 nt)
-14.68066  0.36189877 0.2786389
MGG_00016 | Mo 2-epi-5-epi-valiolone synthase (1739 nt)
-13.50677  0.32379041 0.3759259
MGG_00017 | Mo L-aminoadipate-semialdehyde dehydrogenase (3472 nt) -14.28686
-0.35747999 0.3040601
MGG_00018 | Mo integral membrane protein (2504 nt)
-14.56791  0.45187243 0.1701996
11452 more rows ...
$comparison
[1] "c33"  "con3"
$genes
NULL


> sessionInfo()
R version 2.12.1 (2010-12-16)
Platform: i386-pc-mingw32/i386 (32-bit)
locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United
States.1252
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  tools_2.12.1

I would really appreciate your comments or suggestions.

Many thanks!

Sridhara

-- 
Sridhara G Kunjeti
PhD Candidate
University of Delaware
Department of Plant and Soil Science
email- sridhara@udel.edu
Ph: 832-566-0011

	[[alternative HTML version deleted]]

