Read count vs read count per million (RPM) in Limma or DESeq2
Hi everyone. I am new for bioinformatics and Rstudio. I have just accessed TCGA website and dowloaded data which have 2 columns, read count and read count per million. I want to perform differential expression using Limma or DESeq2 . Which type of expression between read count and read count per million is better to put in these packages?
thank you all!!
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Michael Dondrup
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Emily •
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Emily •
1 answer
You should use the raw read counts. The packages will perform library size normalization themselves.
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