Hi
I have rna sequence data for 4 biological samples: A_stim, A_back, B_stim and B_back. Ultimately, I would like to measure differential expression between 2 experimental conditions A and B. Before I can do this I have to subtract background counts for the two conditions i.e. subtract A_back from A_stim, and B_back from B_stim. I guess before I can subtract, I have to first normalise the samples e.g. convert to RPKM values, and then perform differential expression analysis on the subtracted RPKM values?? Does this seem like a valid way of doing the analysis? I usually use edgeR or DGEseq for differentail analysis, but I don't think they accept RPKM values?
Any thoughts on this would be appreciated.
Thanks,
I have rna sequence data for 4 biological samples: A_stim, A_back, B_stim and B_back. Ultimately, I would like to measure differential expression between 2 experimental conditions A and B. Before I can do this I have to subtract background counts for the two conditions i.e. subtract A_back from A_stim, and B_back from B_stim. I guess before I can subtract, I have to first normalise the samples e.g. convert to RPKM values, and then perform differential expression analysis on the subtracted RPKM values?? Does this seem like a valid way of doing the analysis? I usually use edgeR or DGEseq for differentail analysis, but I don't think they accept RPKM values?
Any thoughts on this would be appreciated.
Thanks,
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