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).
That the question for the interaction of "treatment" and "genotype". In limma you would specify the model as usual, as logExpr ~ treatment*genotype, and the coefficients of the interaction (treatment:genotype) will tell you the difference of the treatment-induced DE between the 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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