Showing : pgsea • reset
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Extract info from smc object
PGSEA smc object
7.8 years ago da.de ▴ 30
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PGSEA Steps Using Bioconductor
microarray pgsea
updated 9.7 years ago by ★ 8.2k • written 9.7 years ago by • 0
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Running the GSEA algorithm
Microarray GeneSetEnrichment PGSEA GSEABase GSRI SeqGSEA Microarray GeneSetEnrichment GSRI
updated 11.6 years ago by ★ 13k • written 11.6 years ago by ▴ 70
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Running the GSEA algorithm
Infrastructure PGSEA GSEABase SeqGSEA Infrastructure PGSEA GSEABase SeqGSEA
updated 11.6 years ago by ★ 1.3k • written 11.6 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
13.7 years ago Valerie Obenchain ★ 6.8k
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PGSEA and smcPlot
GO hgu133plus2 PGSEA GO hgu133plus2 PGSEA
14.2 years ago Valerie Obenchain ★ 6.8k
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PGSEA and smcPlot
GO hgu133plus2 PGSEA GO hgu133plus2 PGSEA
14.3 years ago Iain Gallagher ▴ 930
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PGSEA and Ruuid
Ruuid PGSEA Ruuid PGSEA
16.8 years ago Daniel Klevebring ▴ 80
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Loading the PGSEA package.
PGSEA PGSEA
updated 16.8 years ago by ▴ 90 • written 16.8 years ago by ▴ 20
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a couple of questions on PGSEA package and GSEA
PGSEA PGSEA
updated 17.2 years ago by ▴ 210 • written 17.2 years ago by ★ 1.2k
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ENTREZ identifiers for PGSEA
GO lumi PGSEA GO lumi PGSEA
updated 17.3 years ago by ▴ 90 • written 17.3 years ago by ▴ 370
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PGSEA question
probe PGSEA probe PGSEA
updated 17.7 years ago by ▴ 210 • written 17.7 years ago by ▴ 70
12 results • Page 1 of 1
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Answer: Using DESeq2 for age prediction by ATpoint ★ 5.0k
The package has no such inbuilt function but you are free to use the vst (or any normalized) counts to train a regression model or classifi…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
Aaron already answered your question. If you have an HDF5 file, it will be read in as a `TENxMatrix` object, which isn't actually read in -…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by dan.gatti • 0
Very strange. We have the same package versions. I tried adding the mtx.class, type, and delayed arguments, but it's still making the coun…
Comment: DESeq2 for candidate gene analysis by piffelpaff ▴ 20
thank you so much for answering Dr. Love!
Answer: DESeq2 for candidate gene analysis by Michael Love 43k
Your plan 1 is reasonable. Run DESeq2 on the whole dataset to obtain size factors and moderated dispersion estimates and then extract the u…
Votes
A: Multi-level experiments in Limma
Answer: Should voomWithQualityWeights still be used when the sample-specific weights var
Answer: DESeq2 for candidate gene analysis
DESeq2 for candidate gene analysis
Answer: DESeq2 for candidate gene analysis
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