Showing : goseq • reset
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goseq - overrepresented p-values (Alicia Oshlack)
GO Category goseq GO Category goseq
14.6 years ago Gu Mi ▴ 30
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goseq - overrepresented p-values
GO Category goseq GO Category goseq
updated 14.6 years ago by ▴ 100 • written 14.6 years ago by ▴ 30
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Visualising the GO structure (RNA-seq) using topGO, and goseq
Microarray GO Visualization graph topGO goseq Microarray GO Visualization graph topGO
14.8 years ago Paolo Sonego ▴ 140
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goseq: gene universe
GOstats goseq GOstats goseq
updated 14.8 years ago by ★ 2.0k • written 14.8 years ago by ★ 6.0k
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goseq problem
edgeR goseq edgeR goseq
14.8 years ago Naomi Altman ★ 6.0k
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3.2k
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goseq KEGG testing?
Pathways GO PROcess Category goseq Pathways GO PROcess Category goseq
updated 14.8 years ago by ▴ 40 • written 14.8 years ago by ★ 2.0k
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Can I know the number of genes in enriched GO category using GOseq
GO annotate Category goseq GO annotate Category goseq
updated 14.9 years ago by ▴ 40 • written 14.9 years ago by ▴ 150
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GO with R and Bioconductor
Transcription Annotation GO GOstats biomaRt topGO GSEABase goseq Transcription Annotation
14.9 years ago Duke ▴ 210
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2.9k
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GO with R and Bioconductor
Transcription GO GOstats biomaRt topGO goseq Transcription GO GOstats biomaRt topGO
updated 14.9 years ago by 6.7k • written 14.9 years ago by ▴ 210
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Error GOseq
goseq goseq
updated 14.9 years ago by ▴ 40 • written 14.9 years ago by ▴ 150
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1.5k
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Error in package goseq
Organism goseq Organism goseq
15.4 years ago Joydeep Mitra ▴ 10
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[A question on goseq package with UCSC known gene ID]
GO goseq GO goseq
15.8 years ago sunghee OH ▴ 50
162 results • Page 4 of 4
Recent ...
Replies
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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