I am currently analyzing some RNASeq data from TCGA - which is data that has been processed by RSEM and normalized using a basic quantile normalization. Having this data, I wanted to perform some differential expression testing comparing two groups and thought of using limma to serve this purpose.
However, I am currently adding a pseudocount of 1 to all my normalized counts prior to taking the log2 transform. While this is an easy solution - it is not always the best one. I realize voom transforms are meant to pre-process the RNASeq counts prior to running a linear model, but can you give voom normalized counts instead of raw counts? The documentation makes me think that it only takes in raw counts, and does the normalization internally.
Any feedback would be much appreciated