Entering edit mode
Guest User ★ 12k@guest-user-4897
Last seen 7.1 years ago
Hello, I have ~100 RNA seq-samples from the same organism, but they include different experiments (each experiment of 6-16 samples). I would like to put all together into our RNA seq pipeline, that includes mapping, htseq count and DESeq. Differential expression comparisons will be done of course only between samples of a single experiment (due to possible batch effects). However, will it be a good idea to normalize all samples together? The assumption behind the normalization is that most genes are not differentially expressed, but between different experiments the variability might be higher. Therefore I wanted to ask your opinion on doing the normalization on such a large combined data-set. Thank you, Gilgi -- output of sessionInfo(): none -- Sent via the guest posting facility at bioconductor.org.