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Answer: BiomaRt Possible Ensembl SSL connectivity problems detected.
by
Mike Smith
★ 6.5k
You're running a pretty old version of R and Bioconductor (it's from October 2020). Unfortunately the uswest mirror of Ensembl has been re…
Comment: Size factor normalized counts for between sample comparisons - correct?
by
boczniak767
▴ 740
Thank you @mikelove and @atpoint for help :-)
Comment: More significant genes after lfcShrink in DEseq2?
by
m.orlov
• 0
Hello and thank you for taking the time to answer my question! That's a good point, re threshold vs shrinkage. I know under regular conditi…
Answer: Understanding Contrasts and Interaction in DESeq2 for 2 genotypes, 2 treatments
by
BioinfGuru
▴ 70
This [guide to designs and contrasts in DESeq2][1] is great. Take a look at section 3: Two factors with interaction. It also has a great c…
Comment: Size factor normalized counts for between sample comparisons - correct?
by
Michael Love
42k
The reason i don't prefer SD/mean is that SD is noisy especially when counts are low. So you can get a large value from small count genes j…
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Comment: Size factor normalized counts for between sample comparisons - correct?
Answer: Size factor normalized counts for between sample comparisons - correct?
Comment: Size factor normalized counts for between sample comparisons - correct?
A: How to deal with low-depth RNA-Seq within DESeq2 or edgeR
Answer: voom does not seem to properly correct for library size
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