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News:
Announcing the GBCC2025 Logo Design Contest!
Conference
Community
Galaxy
GBCC2025
Bioconductor
14 months ago
Maria Doyle
▴ 110
0
votes
2
replies
1.6k
views
DESeq2 analysis on Galaxy. PCA plot shows my replicates do not cluster and large intragroup variability
DESeq2
Galaxy
pca
updated 2.9 years ago by
swbarnes2
★ 1.4k • written 2.9 years ago by
mbxdn1
• 0
0
votes
1
reply
1.4k
views
Controlling for sex variance in Galaxy DESeq2
DESeq2
RNASeq
Galaxy
updated 3.9 years ago by
Michael Love
43k • written 3.9 years ago by
István
• 0
0
votes
3
replies
2.4k
views
StringTie output as Ballgown input
ballgown
StringTie
galaxy
rnaseq
updated 3.6 years ago by
Kevin Blighe
★ 4.0k • written 5.5 years ago by
lakshmi9c
• 0
0
votes
1
reply
838
views
deseq2 for enrichments between different subcellular fractions?
deseq2
galaxy
updated 5.8 years ago by
Michael Love
43k • written 5.8 years ago by
mikelirastor
• 0
1
vote
3
replies
1.9k
views
Running DESeq2 inside local Galaxy instance
deseq2
galaxy
8.7 years ago
gkuffel
▴ 10
0
votes
2
replies
1.8k
views
Data analysis in R
bioconductor
next-generation sequencing
galaxy
updated 9.1 years ago by
Lucas Schiffer
▴ 240 • written 9.1 years ago by
efraim.culfa
• 0
0
votes
4
replies
5.0k
views
Using DESeq2 inside Galaxy
rnaseq
galaxy
deseq2
updated 9.8 years ago by
Michael Love
43k • written 9.9 years ago by
Marcelo Pereira
▴ 70
0
votes
2
replies
1.6k
views
Inverting order of groups when using DESeq2
DESeq2
Galaxy
updated 9.8 years ago by
Michael Love
43k • written 9.8 years ago by
Marcelo Pereira
▴ 70
9 results • Page
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Comment: DESeq2 - how many surrogate variables from svaseq, use of lfcshrink
by
ja569116
• 0
Hi @atpoint Thanks for the information. Could you please expand on when to use adjusted p-values vs nominal p-values. My understanding was …
Answer: limpa analysis advice
by
Gordon Smyth
53k
It is actually very hard to estimate the DPC from observed data, because the curve is function of unobserved intensities rather than a func…
Answer: When to use edgeR or limma
by
Gordon Smyth
53k
The short answer is that we generally prefer edgeR for applications with lots of small counts and limma for complex designs with random eff…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry
by
Gordon Smyth
53k
I updated the above answer today.
Answer: When to use edgeR or limma
by
James W. MacDonald
68k
I would use edgeR's quasi-likelihood model for any analysis with a smaller number of observations (like 3 vs 3 or similar), but if you have…
Votes
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
A: deseq2 - paired samples in 2 sequencing types with very different library sizes
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Thomas Girke
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