Hi,

I need some help analyzing my first RNAseq data. I am new to R and DESeq2 and I have been reading manuals for both. Still, I find it very difficult to figure out what I have to do. I would appreciate any help!

Goal of the experiment: see if the wild type (WT) and the mutant (MT) have differences in their transcription when treated with A, B or C.

Information about what I am working with:

Input file: RNAseq raw count file (plain text)

Sample number: 12

Condition (treatment): 3 types of treatment (A,B and C)

Condition2 (genetic background): 2 (WT and MT)

Repetition number per condition: 2

The header of the raw count file looks like this:

ID    WT_A    WT_A    WT_B    WT_B    WT_C    WT_C    MT_A    MT_A    MT_B    MT_B    MT_C    MT_C

The first column contains the gene names.

Here is what I have so far:

#Set the working directory and load the libraries
setwd("~/RNAseq")
library("Biobase")
library("DESeq2")
library("edgeR")

#Reads the file.
#header=true means that the first row is a header.
#row.names=1 means that the first row contains the gene (in this case) names.
j <- read.delim("~/RNAseq/exp1.mat", header=T, row.names=1)

#Remove rows with no reads
jf <- j[rowSums(counts(j)) > 1, ] 

#data.frame contains the information about the samples
dafa = data.frame(row.names = colnames(jf),
                  condition = c("A","A","B","B","C","C","A", "A","B","B","C","C"),
                 condition2 = c("WT","WT","WT","WT","WT","WT", MT","MT","MT","MT","MT","MT") )

... and then I don't know what to do. Can you please give me some hints?