Showing : seqgsea • reset
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Running the GSEA algorithm
Infrastructure PGSEA GSEABase SeqGSEA Infrastructure PGSEA GSEABase SeqGSEA
updated 11.8 years ago by ★ 1.3k • written 11.8 years ago by ▴ 680
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accounting for gene length with SeqGSEA
goseq SeqGSEA goseq SeqGSEA
updated 10.2 years ago by • 0 • written 12.6 years ago by ▴ 110
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Running the GSEA algorithm
Microarray GeneSetEnrichment PGSEA GSEABase GSRI SeqGSEA Microarray GeneSetEnrichment GSRI
updated 11.8 years ago by ★ 13k • written 11.8 years ago by ▴ 70
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install SeqGSEA problem
seqgsea
updated 9.4 years ago by 25k • written 9.4 years ago by • 0
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Including sva results in SeqGSEA with data with batch effect
limma deseq2 seqgsea sva deseq
6.5 years ago kentfung ▴ 20
5 results • Page 1 of 1
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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
Answer: When to use edgeR or limma
A: deseq2 - paired samples in 2 sequencing types with very different library sizes
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