Showing : PGSEA • reset
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Extract info from smc object
PGSEA smc object
7.0 years ago da.de ▴ 30
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PGSEA Steps Using Bioconductor
microarray pgsea
updated 8.9 years ago by ★ 8.2k • written 8.9 years ago by • 0
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Running the GSEA algorithm
Microarray GeneSetEnrichment PGSEA GSEABase GSRI SeqGSEA Microarray GeneSetEnrichment GSRI
updated 10.8 years ago by ★ 13k • written 10.8 years ago by ▴ 70
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Running the GSEA algorithm
Infrastructure PGSEA GSEABase SeqGSEA Infrastructure PGSEA GSEABase SeqGSEA
updated 10.8 years ago by ★ 1.3k • written 10.8 years ago by ▴ 660
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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
12.9 years ago Valerie Obenchain ★ 6.8k
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PGSEA and smcPlot
GO hgu133plus2 PGSEA GO hgu133plus2 PGSEA
13.4 years ago Valerie Obenchain ★ 6.8k
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PGSEA and smcPlot
GO hgu133plus2 PGSEA GO hgu133plus2 PGSEA
13.5 years ago Iain Gallagher ▴ 930
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PGSEA and Ruuid
Ruuid PGSEA Ruuid PGSEA
16.0 years ago Daniel Klevebring ▴ 80
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Loading the PGSEA package.
PGSEA PGSEA
updated 16.0 years ago by ▴ 90 • written 16.0 years ago by ▴ 20
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a couple of questions on PGSEA package and GSEA
PGSEA PGSEA
updated 16.4 years ago by ▴ 210 • written 16.4 years ago by ★ 1.2k
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ENTREZ identifiers for PGSEA
GO lumi PGSEA GO lumi PGSEA
updated 16.5 years ago by ▴ 90 • written 16.5 years ago by ▴ 370
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PGSEA question
probe PGSEA probe PGSEA
updated 16.9 years ago by ▴ 210 • written 16.9 years ago by ▴ 70
12 results • Page 1 of 1
Recent ...
Replies
Comment: Why did PCA plots look exactly the same after adjusting for batch covariate in D by James W. MacDonald 67k
How you analyze your data is up to you. But do note that Subset * Conditions implies that you want to find genes that respond to stimulus d…
Comment: MBDseq analysis using qsea package by kf • 0
Hi Matthias, Happy new year! I wondered if it is possible to retrieve normalized value from each samples? makeTable seems only return beta…
Comment: Why did PCA plots look exactly the same after adjusting for batch covariate in D by Quang • 0
Hi, James. I forgot to mention, but yes, I did run `DESeq2::DESeq()`. So, I ran `DESeq2::DESeqDataSetFromHTSeqCount`, then `DESeq2::DESeq()…
Answer: Why did PCA plots look exactly the same after adjusting for batch covariate in D by ATpoint ★ 4.6k
It's an FAQ in the vignette: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#why-after-vst-are-there-s…
Comment: Deseq2, enrichGO and ensembl ID by James W. MacDonald 67k
I am not sure I understand. You say that a unique Ensembl ID maps to multiple gene symbols. That doesn't mean you have two genes (it's just…
Votes
A: Trajectory analysis for single cell sequencing
Answer: Annotation with org.Hs.eg.db Genome Build 38
Answer: Annotation with org.Hs.eg.db Genome Build 38
Answer: Considerations behind the choice of RNAseq Differential Expression Analysis Tool
A: goana limma- extract list of DE genes and genes in the enriched GO terms?
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