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
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