Bioconductor Limma-trend

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limma voom limma-trend

updated 7.5 years ago by Gordon Smyth 50k • written 7.5 years ago by maltethodberg ▴ 180

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2.2k

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tximport limma limma-trend edgeR

updated 6.6 years ago by Aaron Lun ★ 28k • written 6.6 years ago by Jenny Drnevich ★ 2.0k

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6.2k

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limma limma voom limma-trend

updated 7.4 years ago by Gordon Smyth 50k • written 7.4 years ago by Nik Tuzov ▴ 80

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limma-trend limma

updated 5.8 years ago by Aaron Lun ★ 28k • written 5.8 years ago by Jenny G • 0

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limma limma-trend voom RNASeq

2.5 years ago • updated 2.4 years ago Tyler Sagendorf ▴ 10

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limma voom limma-trend

updated 6.2 years ago by max.moldovan • 0 • written 7.3 years ago by b.nota ▴ 360

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894

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limma limma-trend limma-voom

updated 3 months ago by floriandeckert ▴ 30 • written 17 months ago by hainct • 0

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2.1k

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limma-trend duplicatecorrelation arrayweights limma

updated 6.6 years ago by Gordon Smyth 50k • written 6.6 years ago by maltethodberg ▴ 180

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2.0k

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MNNCorrect scMerge limma-trend

updated 3.0 years ago by Gordon Smyth 50k • written 3.1 years ago by hainct • 0

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830

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search tximport limma-trend

updated 6.2 years ago by James W. MacDonald 65k • written 6.2 years ago by Jenny Drnevich ★ 2.0k

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Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0

Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …

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 (as at 4 May 2024). In the meantime, you could consider using the goana() and kegga() …

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…

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Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-

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

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