Hi,
I have an RNAseq experiment with 9 different treatments as triplicates. My problem is that if I load all 9 treatments into DESeq I get 2695 DE genes for a given treatment. If I am loading only the libraries of that treatment and the control I get 314 DE genes. EstimateDispersions sharingMode was maximum.
Later in the analysis I want to build intersects and compare the genes between the different treatments.
Since I am not familiar with the dispersion concept I want to ask what the "correct" way to do the analysis is? Should I use all the data in one analysis or do each treatment separately?
Thank you!
I have an RNAseq experiment with 9 different treatments as triplicates. My problem is that if I load all 9 treatments into DESeq I get 2695 DE genes for a given treatment. If I am loading only the libraries of that treatment and the control I get 314 DE genes. EstimateDispersions sharingMode was maximum.
Later in the analysis I want to build intersects and compare the genes between the different treatments.
Since I am not familiar with the dispersion concept I want to ask what the "correct" way to do the analysis is? Should I use all the data in one analysis or do each treatment separately?
Thank you!
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