Many differential expression packages out there require the raw_count as their input but I want to use my normalized values as input. From what I can find limma+voom can handle normalized values. Are there any other package that allows me to use normalized values?
I've tried using DESeq2 despite reading various comments saying it only works with raw_count values but when I looked at the fold change values and manually inspecting the normalized values, the fold change output seems pretty reasonable. Why is it that you can't use normalized values with DESeq2?