Showing : gsva • reset
1
vote
2
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394
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Can limma be used with module eigengenes instead of genes?
limma WGCNA GSVA
written 5 months ago by ▴ 20
1
vote
2
replies
1.7k
views
GSVA 1.52.2 (new API) nb of workers?
parallelize workers GSVA
written 19 months ago by • 0
1
vote
1
reply
2.2k
views
GSVA Error Code "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct" and "unused arguments (exprsData = as.matrix(rna_seq_sub), gset.idx…
GSVA
updated 10 months ago by ★ 5.0k • written 10 months ago by • 0
5
votes
5
replies
2.4k
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Unused arguments error without used arguments in GSVA?
GSVA
updated 9 months ago by • 0 • written 11 months ago by • 0
1
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5
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1.3k
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Identifying potentially associated gene set to drug response using GSVA
drug RNASeq GSVA
written 14 months ago by • 0
0
votes
1
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1.2k
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
written 20 months ago by ▴ 20
1
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6
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7.8k
views
GSVA on RNAseq data
gsva rnaseq
updated 11 months ago by ★ 3.4k • written 6.8 years ago by ▴ 60
7 results • Page 1 of 1
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Replies
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…
Answer: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
The short answer is that limpa reads standard feature-level intensities from Spectronaut or other quantifications tools. limpa is designed …
Comment: Question about the filterByExpr function inputs in edgeR by mohammedtoufiq91 ▴ 10
@gordonsmyth Noted, thank you very much.
Votes
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
Comment: Question about the filterByExpr function inputs in edgeR
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