Bioconductor RNA Seq

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3.2k

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batch effect limma rna seq DE

updated 4.0 years ago by Steve Lianoglou ★ 13k • written 4.0 years ago by svlachavas ▴ 830

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2.6k

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deseq2 mahattan plot RNA Seq

updated 3.6 years ago by bernatgel ▴ 150 • written 4.5 years ago by adeler001 • 0

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1.9k

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rna seq trimmomatic trimming adapter trimming paired analysis

5.0 years ago Mozart ▴ 30

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1.6k

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heatmap.2 hierarchical clustering microarray RNA seq DEG

6.2 years ago lawarde.ankita1 ▴ 30

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1.3k

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limma voom RNA Seq Time-course experiments

updated 4.9 years ago by Aaron Lun ★ 28k • written 4.9 years ago by mahes.muniandy • 0

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964

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RNA seq wgcna

updated 4.9 years ago by Peter Langfelder ★ 3.0k • written 4.9 years ago by agustin.gonvi ▴ 20

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947

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volcano plot rna seq

updated 4.7 years ago by Michael Love 41k • written 4.7 years ago by adeler001 • 0

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894

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edger RNA Seq

updated 4.4 years ago by James W. MacDonald 65k • written 4.4 years ago by abf ▴ 30

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885

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sgseq alternative splicing rna seq

updated 4.4 years ago by Leonard Goldstein ▴ 200 • written 4.4 years ago by 116100016 • 0

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780

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rna seq SGSeq Alternative splicing

updated 4.6 years ago by Leonard Goldstein ▴ 200 • written 4.6 years ago by 116100016 • 0

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650

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RNA seq cpm

updated 4.1 years ago by Kevin Blighe ★ 3.9k • written 4.1 years ago by isabel.pieterse • 0

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550

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deseq2 likelihood ratio rna seq wald test

updated 4.6 years ago by Michael Love 41k • written 4.6 years ago by adeler001 • 0

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497

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rna seq

4.5 years ago adeler001 • 0

13 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!

Votes

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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