I want to identify differentially expressed genes between two timepoints, from high-throughput digital gene expression profiling (Helicos), in mammalian cells. Sometimes I have replicates, sometimes not (depending on experiment/dataset).
I read about three programs which seem suitable, edgeR, DESeq and bayseq; however the differences between these three programs seem quite subtle to me.
What are the central differences between these three programs? How can I choose the one which fits my analysis needs best?
I read about three programs which seem suitable, edgeR, DESeq and bayseq; however the differences between these three programs seem quite subtle to me.
What are the central differences between these three programs? How can I choose the one which fits my analysis needs best?
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