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Comment: Small RNA-seq Analysis DESEQ2 : Unexpected Significance
by
ATpoint
★ 3.6k
"Raw" counts, so you're plotting un-normalized data, hence plots have no meaning in terms of groupwise comparisons. Use the `normTransform`…
Answer: In DiffBind, dba.blacklist changes the minOverlap parameter
by
Sam
▴ 10
I have found a workaround : running dba.blacklist **after** running dba.count (while running dba.count with minOverlap=1). ``` dbObj_co…
Comment: Small RNA-seq Analysis DESEQ2 : Unexpected Significance
by
samer
• 0
By applying the log2 transformation to the raw counts of small RNAS AND after adding 1 to each count, the resulting values often approximat…
Comment: Small RNA-seq Analysis DESEQ2 : Unexpected Significance
by
samer
• 0
and sometimes in other count plots we observe a difference between the counts of the 2 conditions (ON/OFF) where it should be significant b…
Comment: Small RNA-seq Analysis DESEQ2 : Unexpected Significance
by
ATpoint
★ 3.6k
What is `Log2 Counts + 1`? Please show code for the plots. And please remove the comments and move everything to the toplevel question usin…
Votes
Answer: WGCNA documentation not available
Comment: Can the limma package be applied to Log2 RUV-normalized data?
Comment: Can the limma package be applied to Log2 RUV-normalized data?
Answer: Correct the batch effect in methylation analysis in R
Comment: Why is DMRcate not available for Bioconductor version 3.18?
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