Hi I'm trying to analyze RNA-seq data of multiple ICGC projects. I want to remove batch effects of projects with SVA package and algorithm before employing DEseq2 for finding differentially expressed genes and after that network analysis. I have these questions:
1) DEseq2 uses only raw read counts, and it shouldn't be normalized in any way. How can I use SVA output as DEseq2 input? I know that DEseq2 has the ability to get confounding variable (project codes) in its formula but I don't wan't to use it.
2) Should I log transform my raw read counts before using SVA?
3) Can I use microarray and RNA-seq in a single analysis after removing its batch effects by SVA and normalization? Is it a valid analysis? If not, what is the best way to analyze the two datasets as a single dataset? about half of my samples are only in microarray. none of samples are repeated in datasets.