Read count vs read count per million (RPM) in Limma or DESeq2

Question

[Emily]

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!!

[Michael]

Why is this tagged miRNA?

Answer 1

[Michael]

You should use the raw read counts. The packages will perform library size normalization themselves.