Bioconductor Gene set testing

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R DESeq2 gene set testing gene expression

7.5 years ago Jon Bråte ▴ 250

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1.8k

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gene set testing roast mroast differential gene expression bioconductor

9.0 years ago svlachavas ▴ 830

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limma agilent microarrays gene set testing annotation

7.3 years ago Bouzid.a ▴ 20

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limma camera gene set testing ensembl

updated 4.4 years ago by Robert Castelo ★ 3.3k • written 4.4 years ago by Jeremy Beales ▴ 10

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gene set testing camera edger

updated 7.8 years ago by Gordon Smyth 50k • written 7.8 years ago by le2336 ▴ 20

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3.2k

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limma mroast barcodeplot KEGG gene set testing

updated 8.4 years ago by Gordon Smyth 50k • written 8.4 years ago by svlachavas ▴ 830

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1.6k

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EGSEA gene set testing vooma limma voom gsea

7.3 years ago • updated 7.2 years ago Pekka Kohonen ▴ 190

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1.4k

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limma agilent microarrays mroast fry gene tests gene set testing

updated 5.6 years ago by Gordon Smyth 50k • written 5.6 years ago by svlachavas ▴ 830

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limma camera gene set testing

8.0 years ago claire.n.levy ▴ 10

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1.3k

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gage gene set testing

updated 5.9 years ago by Luo Weijun ★ 1.6k • written 5.9 years ago by Aurora ▴ 20

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1.2k

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limma roast statistics source code gene set testing

5.7 years ago Andrea Carenzo • 0

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1.3k

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limma camera cameraPR edgeR gene set testing

updated 5.6 years ago by Gordon Smyth 50k • written 5.6 years ago by jamie.gearing ▴ 60

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624

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mroast camera gene set testing

3.6 years ago svlachavas ▴ 830

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1.3k

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gsea ncrna coexpression gene set analysis gene set testing

8.0 years ago m.fletcher ▴ 20

14 results • Page 1 of 1

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Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k

Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…

Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k

I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …

Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k

It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…

Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k

This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…

Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0

Thank you Tim, this is a great help in getting me started!

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Answer: limma Intercept vs No-intercept models completely changing DMR results?

Answer: CombineArrays for EPIC and EPIC V2

Answer: Too many significant genes when integrating gtex and tcga

Comment: Too many significant genes when integrating gtex and tcga

A: Print Differentially Expressed Exons From Dexseq Results

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