We want to identify genes which have differential expression between sensitive and tolerant genotypes in RNA-seq data by R.
Which package is suitable for our query?
There are several R based packages to do Differential Expression. For example - edgeR, DEseq and so on...Never use student's t-test for doing DGE. Hope this helps..
Thanks for all answers, I have 12 samples of RNA-seq data (2 treats, 2 genotypes and 3 replications). I also used the DEseq package to find DEGs between control and treatment samples in both genotypes but now I want to identify genes with significant differential expression between them (both genotypes).
You can set the follow model and use the appropriate coefficients to identify DGE.
logExpr ~ gt + trt + gt*trt
gt = genotype
trt = treatment
gt*trt = interaction
If you wanted to identify DEG between genotypes then you drop coef 1, between treatment then coef 2 and for gt*treatment you drop coef 3. This is clearly mentioned in DESeq manual.
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