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Comment: Using featureCounts with SAF annotation file gives "Error: only GTF files contai
by
atan
• 0
Thank you! I ended up running it with a gtf on command line, partially because I couldn't figure out how to list multiple files in R for in…
Comment: Using featureCounts with SAF annotation file gives "Error: only GTF files contai
by
atan
• 0
For some reason, that's still not working for me on command line. I ended up figuring out another way around, though, by converting the g…
Answer: LRT, pairwise comparisons and p-value adjustment
by
James W. MacDonald
66k
The convention is to adjust only within comparisons. But as the analyst, that's your call.
Comment: Counter-directional LFC shrinkage
by
ennui
• 0
Thank you for your response. The `ashr` shrinkage indeed preserves more of the original ranks in the data. So if I understand correctly, L…
Comment: Counter-directional LFC shrinkage
by
ennui
• 0
I agree it looks offset (and weird). The data is from NGS, not RNAseq, but we still want to see relative abundance between conditions - I t…
Votes
Reduce the number of nodes appear in the cnetplot of clusterprofiler
A: DESeq2: add annotations (from data frame) to DESeqDataSet
Answer: Error in gseDO function
Comment: what the test method for enrichGO in clusterProfiler?
A: Comparison between two different group's pathway analysis results
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