Hello, I used an RSEM, gene-level count estimates matrix and just rounded the values using the round() function in R to feed them to DESeq2 but the results are very odd (VERY low number of deferentially expressed genes). Is this really a solid way to go about deferential analysis or should I resort to starting from raw data again.
I read multiple threads that suggested that the rounding method, although not optimal, should work fine.
NOTE: The study I got the data from provided the data as RSEM gene-level count matrix and FPKM normalized matrix. I had to use rsem since I know DESeq2 only takes non-normalized counts. The study used an independent t-test on the FPKM file to do the analysis, but I read somewhere that it is highly discouraged.