Bioconductor Multiple comparisons

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17k

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limma illumina differential gene expression multiple comparisons design matrix

8.9 years ago • updated 8.8 years ago svlachavas ▴ 830

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4.0k

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rnaseq multiple comparisons post hoc deseq2

7.9 years ago • updated 7.2 years ago laianavarromartin ▴ 20

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3.4k

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deseq2 multiple comparisons

8.9 years ago annalisa.giampetruzzi • 0

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3.9k

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edger design and contrast matrix multiple factor design multiple comparisons

updated 8.8 years ago by James W. MacDonald 65k • written 8.8 years ago by mouchkam ▴ 20

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1.5k

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deseq2 multiple comparisons contrast

updated 6.4 years ago by James W. MacDonald 65k • written 6.4 years ago by serpalma.v ▴ 60

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5.8k

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edger multiple comparisons anova glm

updated 8.9 years ago by Ryan C. Thompson ★ 7.9k • written 8.9 years ago by chickenchamp4 ▴ 20

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1.3k

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rnaseq pairwise multiple comparisons deseq2

updated 8.2 years ago by Michael Love 41k • written 8.2 years ago by hamaor • 0

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4.9k

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limma design matrix makecontrasts multiple comparisons

7.3 years ago • updated 7.2 years ago annabelle.congras ▴ 10

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926

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deseq2 deseq rna-seq multiple comparisons

updated 5.8 years ago by Michael Love 41k • written 5.8 years ago by rbronste ▴ 60

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870

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edger multifactorial design multiple comparisons differential gene expression

updated 6.2 years ago by Aaron Lun ★ 28k • written 6.2 years ago by svlachavas ▴ 830

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1.9k

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limma multiple factor design multiple comparisons

updated 7.6 years ago by Gordon Smyth 50k • written 7.6 years ago by xluong • 0

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2.1k

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deseq2 rnaseq contrast multiple comparisons fdrtool

8.0 years ago sebastiano.curreli • 0

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1.8k

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deseq2 padj multiple comparisons differential gene expression

updated 7.1 years ago by Michael Love 41k • written 7.1 years ago by tarun2 • 0

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2.8k

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qvalue pvalue r multiple comparisons

updated 7.3 years ago by Storey, John D. ▴ 100 • written 7.3 years ago by tombernardryan ▴ 50

14 results • Page 1 of 1

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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!

Comment: Too many significant genes when integrating gtex and tcga by Michael Love 41k

Yes, this was one of the aspects we highlighted in the 2014 paper, and it's also in the workflow. Check these places first. Also take a st…

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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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