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StageR
•
reset
0
votes
10
replies
1.2k
views
Two treatments, one control
DESeq2
stageR
4 months ago
alephreish
• 0
0
votes
2
replies
595
views
Swimming downstream: transcript fold changes
DEXSeq
stageR
12 months ago
jbono
▴ 10
0
votes
1
reply
725
views
stageR p-adj values of zero
stageR
updated 3.1 years ago by
Koen Van den Berge
▴ 180 • written 3.2 years ago by
giwa.ao
• 0
0
votes
1
reply
996
views
stageR with input from DRIMSeq
DRIMSeq
stageR
updated 5.7 years ago by
Koen Van den Berge
▴ 180 • written 5.7 years ago by
sdvie
• 0
2
votes
4
replies
1.9k
views
stageR: Error in stageWiseAdjustment
stageR
rnaseqDTU
DRIMSeq
DEXSeq
5.8 years ago
d-joester
▴ 20
4
votes
4
replies
1.5k
views
Correct use of Nested/Stage-wise testing with limma/stageR for 3-group design.
limma
stageR
decideTests
updated 5.9 years ago by
Koen Van den Berge
▴ 180 • written 5.9 years ago by
maltethodberg
▴ 180
0
votes
3
replies
1.3k
views
Post-hoc filtering on the standard deviation in proportions
drimseq
rnaseqdtu
stager
updated 6.0 years ago by
Michael Love
43k • written 6.0 years ago by
Jack.Hearn
• 0
1
vote
5
replies
1.8k
views
Plotting Expression of Differential Transcripts plotDEXseq
DEXSeq
StageR
rnaseqDTU
updated 6.1 years ago by
Michael Love
43k • written 6.1 years ago by
rbenel
▴ 40
2
votes
9
replies
2.1k
views
stageR NA in getAdjustedPValues() (method=dtu)
drimseq
stageR
dtu
salmon rna seq
updated 6.4 years ago by
Koen Van den Berge
▴ 180 • written 6.4 years ago by
fiona.dick91
▴ 60
9 results • Page
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Replies
Comment: Differential Expression Genes as Independent Variables
by
Dario Strbenac
★ 1.5k
Also, the reason why gene abundance is the dependent variable and is iterated over is that there are far more genes than there are samples …
Comment: rrvgo::calculateSimMatrix() error
by
Phila
• 0
Thanks for sharing the solution. It helps me. [nced cloud][1] [1]: https://my-ncedcloud-login.us/
Comment: Merge Replicates vs Mixed Model
by
gabriel.hoffman
▴ 170
For your proteomics data, your normalization is correct. I had assumed it was RNA-seq because that is what I think about most. When using…
Comment: What type of counts data to import for performing Isoform analysis in edgeR
by
mohammedtoufiq91
▴ 10
@gordonsmyth I will re-run Salmon with the --numGibbsSamples=50 option. Thank you.
Comment: Differential Expression Genes as Independent Variables
by
Gordon Smyth
52k
Such an analysis cannot be done in limma. Sorry, I cannot tell you how to do it or even whether it is possible.
Votes
Comment: What type of counts data to import for performing Isoform analysis in edgeR
Answer: What type of counts data to import for performing Isoform analysis in edgeR
Transcript-level differential expression using DESeq2
Comment: What type of counts data to import for performing Isoform analysis in edgeR
Answer: What type of counts data to import for performing Isoform analysis in edgeR
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