[BioC] edgeR

[Mark Robinson]

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 at 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 at udel.edu
>> Ph: 832-566-0011
>>
>
>
>
> --
> Sridhara G Kunjeti
> PhD Candidate
> University of Delaware
> Department of Plant and Soil Science
> email- sridhara at udel.edu
> Ph: 832-566-0011
>
> 	[[alternative HTML version deleted]]
>
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