Thanks Sean Davis for your reply.

Yes. I know that #1 = #4 and and #2=#3. I mentioned the 4 categories to
clarify the question.
Here is the code that I wrote:

dge.list <- estimateTagwiseDisp(dge.list, prior.df=50)  #estimate tagwise
dispersion
de.exactTest.tgw <- exactTest(dge.list, dispersion = "tagwise", pair =
c("A", "B"))
resultsTbl.tgw <- topTags(de.exactTest.tgw, n =
nrow(de.exactTest.tgw$table))$table
summary( decideTestsDGE( de.exactTest.tgw , p.value = 0.05 ) )

the summary function will show the following outputs:
 [,1]
-1  207
0  8394
1   359

Based on the documentation, I think that these 207 are upregulated in A.
The 359 genes are upregulated in B .. corrrect?
Now, I want to get the genes of the two groups (207 and 359) and print each
gene set in a file.
In the past couple of hours, I tried to write it as:
rownames(de.exactTest.tgw[decideTestsDGE( de.exactTest.tgw , p.value = 0.05
) == 1]$table)  #show the 359 genes
rownames(de.exactTest.tgw[decideTestsDGE( de.exactTest.tgw , p.value = 0.05
) == -1]$table) #show the 207 genes

I hope this was correct? I am wondering if there is a quick way to remove
the double-quotation from the outputs of previous commands and write it one
gene per line to file

Regards,


On Sat, Apr 13, 2013 at 12:30 AM, Sean Davis <sdavis2@mail.nih.gov> wrote:

> On Fri, Apr 12, 2013 at 4:50 PM, Abdullah khamis
> <abdullahkhamis@gmail.com> wrote:
> > Dear edgeR Community,
> >
> > I have 12 samples that belong to two groups (A and B), 6 samples per
> group,
> > and I want to know which genes are up-regulated in group A and
> > down-regulated in B and vice versa.
> > I use the functions summary() and the function decideTestsDGE() but I
> could
> > not get the summary information about
> > 1) up-regulated genes in Group A
> > 2) down-regulated genes in Group A
> > 3) up-regulated genes in Group B
> > 4) down-regulated genes in Group B
>
> Hi, Abdullah.
>
> You might need to show us what you have tried.  Keep in mind that
> genes in #1 above are the same as genes in #4 and that genes in #2 are
> the same as #3 when you have two groups.
>
> Sean
>

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