Showing : pgsea • reset
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Extract info from smc object
PGSEA smc object
7.2 years ago da.de ▴ 30
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PGSEA Steps Using Bioconductor
microarray pgsea
updated 9.0 years ago by ★ 8.2k • written 9.0 years ago by • 0
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Running the GSEA algorithm
Microarray GeneSetEnrichment PGSEA GSEABase GSRI SeqGSEA Microarray GeneSetEnrichment GSRI
updated 10.9 years ago by ★ 13k • written 10.9 years ago by ▴ 70
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Running the GSEA algorithm
Infrastructure PGSEA GSEABase SeqGSEA Infrastructure PGSEA GSEABase SeqGSEA
updated 10.9 years ago by ★ 1.3k • written 10.9 years ago by ▴ 680
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[Rocky] - R code for PGSEA package to identify differentially expressed genes
GO affy limma GLAD PGSEA GSEABase GO affy limma GLAD PGSEA GSEABase
13.1 years ago Valerie Obenchain ★ 6.8k
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PGSEA and smcPlot
GO hgu133plus2 PGSEA GO hgu133plus2 PGSEA
13.6 years ago Valerie Obenchain ★ 6.8k
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PGSEA and smcPlot
GO hgu133plus2 PGSEA GO hgu133plus2 PGSEA
13.6 years ago Iain Gallagher ▴ 930
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991
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PGSEA and Ruuid
Ruuid PGSEA Ruuid PGSEA
16.1 years ago Daniel Klevebring ▴ 80
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Loading the PGSEA package.
PGSEA PGSEA
updated 16.1 years ago by ▴ 90 • written 16.1 years ago by ▴ 20
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a couple of questions on PGSEA package and GSEA
PGSEA PGSEA
updated 16.5 years ago by ▴ 210 • written 16.5 years ago by ★ 1.2k
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2
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ENTREZ identifiers for PGSEA
GO lumi PGSEA GO lumi PGSEA
updated 16.6 years ago by ▴ 90 • written 16.7 years ago by ▴ 370
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PGSEA question
probe PGSEA probe PGSEA
updated 17.0 years ago by ▴ 210 • written 17.0 years ago by ▴ 70
12 results • Page 1 of 1
Recent ...
Replies
Comment: how many significant figures are there in DESeq2 output by ATpoint ★ 4.7k
If you want consistency then use a fixed software environment like Docker, wirh fixed code and thresholds that make sense. Rounding to near…
Comment: Compare TCGA-PAAD with GTEx gene expression by Jane • 0
why aren't there any answers?
Comment: Too many significant genes when integrating gtex and tcga by Jane • 0
I encountered the same issue: too many DEGs after limma analysis. It is sad that until today we can still see the paper published where GTE…
Comment: how many significant figures are there in DESeq2 output by Matthew McCormack ▴ 180
Thank you for your reply. It is good to know that cutoff of 0.05 means less than 0.05. My concerns are about consistency and reproducibili…
Comment: DiffBind edgeR normalization --- why are the normalization factors all equal to by ATpoint ★ 4.7k
No, normalization factors from edgeR rather than size factors from DESeq2 are not proportional, it's a different concept and implementation…
Votes
A: Unbalanced experiment with multiple samples from each patient.
Unbalanced experiment with multiple samples from each patient.
Answer: Vertical line at A=0, nothing else, on MA plot
Answer: GSVA Error Code "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct
Answer: Group-specific condition effects with individuals nested: matrix is not full ra
Awards • All
Popular Question to svlachavas ▴ 840
Popular Question to Matthew McCormack ▴ 180
Popular Question to James W. MacDonald 68k
Popular Question to shepherl 4.1k
Popular Question to Marco • 0
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