Hello, I recently completed running limma-trend to find differentially expressed genes influenced by the sex, tissue type, and infection status of a plant. For example, one comparison was male infected flowers to female infected flowers. According to limma, there are significant differences in many of my comparisons, but in trying to get the output data, I'm unable to obtain certain information. I'm using this code
tab<-topTable(fit, sort.by="none", adjust.method= "BH", n= Inf, coef = 12) write.table(tab, file = "MIF_FIF.txt", sep = "\t")
to get a file looking at that specific comparison, but this approach only gives me the following output:
"logFC" "AveExpr" "t" "P.Value" "adj.P.Val" "B" "MOEQ000001T1exon1" 0.860344126172371 -2.2168954728788 2.86670254017661 0.0094071156815448 0.0343743208965692 -3.28233021689611 "MOEQ000002T1exon1" 1.74657018568266 -1.89484698082333 3.99972492140815 0.000680711380052985 0.00453880630827772 -0.752598382957659 "MOEQ000002T1exon2" 2.97743301874836 -1.53494458820183 5.18827888515825 4.19384639412824e-05 0.000573395231909479 1.99452393543233
In addition to this information, I'd like to have the output contain the mean expression values for each group, so a column for mean expression in male infected flowers and a column for the mean expression in female infected flowers. Additionally, I'd like to have a column with the log2FC as well. Does anyone know how to go about getting all of this information out of limma into one result file per comparison? Thanks very much!