Hi. I had just started learning R and have been working on a script on EdgeR for Illumina data to analyze differential expression. SO I have two different samples with two tissues from each for which I have count data set for each one of them. I am intersted in comparing one tissue from one sample with other one from another sample (as well interested to compare within a sample). Below is the script I was trying to use, which gives error. Since I am new to this R programming, I am not able to figure what or where the problem is. I would really appreciate if someone could help me with this.Thanks.
library(edgeR)
library(limma)
setwd("C:\\cygwin\\home\\Prabhakaran")
load("test1.txt")
raw.data <- read.table(file="test1.txt", header=TRUE)
names(raw.data)
d <- raw.data[, 2:3]
rownames(d) <- raw.data[ ,1]
sample <- factor(R91+92_LFE_Hits, X95+96_clark_E_hits)
d <- estimateCommonDisp(d)
et <- exactTest(d)
topTags(et)
etTag = rownames(topTags(et)$table)
sum(et$table$p.value <0.05)
sum(p.adjust(et$table$p.value,method="BH") < 0.1)
good = sum(et$table$p.value <0.05)
goodList = topTags(et, n=good)
sink("output1.csv")
goodList
sink()
library(edgeR)
library(limma)
setwd("C:\\cygwin\\home\\Prabhakaran")
load("test1.txt")
raw.data <- read.table(file="test1.txt", header=TRUE)
names(raw.data)
d <- raw.data[, 2:3]
rownames(d) <- raw.data[ ,1]
sample <- factor(R91+92_LFE_Hits, X95+96_clark_E_hits)
d <- estimateCommonDisp(d)
et <- exactTest(d)
topTags(et)
etTag = rownames(topTags(et)$table)
sum(et$table$p.value <0.05)
sum(p.adjust(et$table$p.value,method="BH") < 0.1)
good = sum(et$table$p.value <0.05)
goodList = topTags(et, n=good)
sink("output1.csv")
goodList
sink()
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