Hello All
I am really new to edgeR so please excuse me if the question is trivial. I am trying to run edgeR to perform some statistical analysis on RNA-Seq data. I was trying to follow an example on edgeR wiki version and adapting it to my experiment. However, I encountered a problem at the initial stage where I am trying to get edgeR to read my data in a text file. My code has been written below. Code lines are in italics. Error is in bold.
#raw data
library(edgeR)
Loading reqraw.data<-read.table(file="All_Samples1.txt",header=TRUE)
head(raw.data)
Geneid DP12101 DP12102 DP1251 DP1252 DP1201 DP1202 DH101 DH102 DH51 DH52
1 rna22510 0 0 0 0 0 0 0 0 0 0
2 rna22511 0 0 0 0 0 0 0 0 0 0
3 rna22512 0 0 0 0 0 0 0 0 0 0
4 rna22513 0 0 0 0 0 0 0 0 0 0
5 rna22514 0 0 0 0 0 0 0 0 0 0
6 rna22515 0 0 0 0 0 0 0 0 0 0
( A background of the example I am following: The raw data in the example has an extra column in its column specifying the length of the reads. The code in that example is same as the one I used below.
#reading data into edgeR
counts<-raw.data[,-c(1,ncol(raw.data))]
rownames(counts)<-raw.data[,1]
colnames(counts) <- paste (c (rep ("DP_10",2), rep("DP_5",2), rep("DP_0",2), rep("DH_10",2), rep("DH_5",2)), c(1:2,1:2,1:2,1:2,1:2), sep=" ")
Error in `colnames<-`(`*tmp*`, value = c("DP_10 1", "DP_10 2", "DP_5 1", : 'names' attribute [10] must be the same length as the vector [9]
I believe that my error is the presence of 10 attributes in code but there are only 9 columns. And it seems to me that somewhere in the code there is a line asking it to skip the final column. Since I am new it would be great if you could help me correct the error.
PS: I did proceed creating a dummy column at the end but I would like to learn why I was not able to correct it without adding the dummy column. I tried different variations of the code trying to omit 1 in the first two lines, but was not successful.
Thank You
