Hello Mark,
Thanks you very much for the information.

Many thanks!
Sridhara

On Sat, Mar 5, 2011 at 1:01 AM, Mark Robinson <mrobinson@wehi.edu.au> wrote:

>
> Try using one 'DGEList' with all your data, (all the usual steps,) then
> choose what pair you want to test with:
>
> de.3 <- exactTest(d, pair=c("F0","F3"))
> de.6 <- exactTest(d, pair=c("F0","F6"))
>
> Also see ?exactTest and the user's guide.
>
> Cheers,
> Mark
>
> > In continuation with my previous email. Here are the codes that I have
> > used.
> >> setwd("C:/Users/SRIDHARA/Documents/Sequence
> > analysis/02-Pphaseoli/Pphaseoli-ExpressionDataTable/Filtered")
> >> library(edgeR)
> >> raw.data <- read.delim("Pp-Rdata.txt")
> >> names(raw.data)
> > [1] "ID"  "F0a" "F0b" "P3a" "P3b" "P6a" "P6b" "LEN"
> >> d <- raw.data[, 2:7]
> >> rownames(d) <- raw.data[,1]
> >> group <- c(rep("F0", 2), rep("P3", 2)rep("P6", 2))
> > Error: unexpected symbol in "group <- c(rep("F0", 2), rep("P3", 2)rep"
> >> group <- c(rep("F0", 2), rep("P3", 2), rep("P6", 2))
> >> group
> > [1] "F0" "F0" "P3" "P3" "P6" "P6"
> >> d <- DGEList(counts = d, group = group)
> > Calculating library sizes from column totals.
> >> d <- estimateCommonDisp(d)
> >> de.com <- exactTest(d)
> > Comparison of groups:  P3 - F0
> >> d <- estimateTagwiseDisp(d, prior.n = 10, grid.length = 500)
> > Using grid search to estimate tagwise dispersion.
> >
> > where as when if I want to analyze between F0 and P6 the codes that I
> used
> > are:
> >> d6 <- extimageCommonDisp(d, pair = c("F0", "P6"))
> > Error: could not find function "extimageCommonDisp"
> >> d6 <- estimateCommonDisp(d, pair = c("F0", "P6"))
> > Error in estimateCommonDisp(d, pair = c("F0", "P6")) :
> >   unused argument(s) (pair = c("F0", "P6"))
> >
> > Thanks,
> > Sridhara
> >
> >
> > On Fri, Mar 4, 2011 at 8:17 PM, Sridhara Gupta Kunjeti
> > <sridhara@udel.edu>wrote:
> >
> >> Hello,
> >> I want to analyze DGE for three different groups (for eg., gpA, B and
> >> C). I
> >> know that this will analyze only two groups at a time, which is fine for
> >> my
> >> analysis. But, I have the counts for all the groups in one txt  file.
> >> When I
> >> run exact test, it will analyze for gp A- gp B. My question is if I want
> >> to
> >> run the analysis for gpA and gp C what command do I need to use.
> >>
> >> Alternatively, if I load the data for two gps at time, will the p.value
> >> change as against to when all the groups are loaded into R.
> >>
> >> Any help or suggestions will be appreciated.
> >>
> >> Thanks,
> >> Sridhara
> >>
> >>
> >>
> >> --
> >> Sridhara G Kunjeti
> >> PhD Candidate
> >> University of Delaware
> >> Department of Plant and Soil Science
> >> email- sridhara@udel.edu
> >> Ph: 832-566-0011
> >>
> >
> >
> >
> > --
> > 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]]
> >
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>
>
>
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