Bioconductor EBayes

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topTable MicroarrayData ebayes limma Microarray

3.8 years ago snijesh ▴ 200

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limma eBayes decideTests topTable

updated 4.8 years ago by Gordon Smyth 52k • written 4.8 years ago by irene.roman • 0

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limma eBayes

updated 5.8 years ago by Gordon Smyth 52k • written 5.8 years ago by Sebastian Hesse ▴ 70

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Limma ebayes bayesian ls

updated 6 months ago by Gordon Smyth 52k • written 6.2 years ago by CantExitVIM ▴ 10

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model.matrix lmFit eBayes GEOquery limma

6.8 years ago darthratus • 0

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ebayes limma bioconductor

updated 7.1 years ago by Gordon Smyth 52k • written 7.1 years ago by reventropy2003 ▴ 10

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ebayes limma

7.1 years ago peirinl • 0

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eBayes limma error

updated 7.4 years ago by James W. MacDonald 67k • written 7.4 years ago by calen.p.ryan • 0

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ebayes limma voom

7.8 years ago bag59 • 0

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limma ebayes

updated 19 months ago by Gordon Smyth 52k • written 7.9 years ago by cemcdono • 0

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limma ebayes

updated 9.1 years ago by Aaron Lun ★ 28k • written 9.1 years ago by bharata1803 ▴ 60

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limma ebayes statistical inference

updated 9.3 years ago by Gordon Smyth 52k • written 9.3 years ago by ssrajan86 • 0

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limma eset error ebayes

updated 9.4 years ago by James W. MacDonald 67k • written 9.4 years ago by Vani ▴ 20

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ebayes expression affymetrix pd.hugene.2.0.st limma

updated 9.9 years ago by Gordon Smyth 52k • written 9.9 years ago by Paulo Nuin ▴ 200

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Comment: Differential Expression Genes as Independent Variables by Dario Strbenac ★ 1.5k

Also, the reason why gene abundance is the dependent variable and is iterated over is that there are far more genes than there are samples …

Comment: rrvgo::calculateSimMatrix() error by Phila • 0

Thanks for sharing the solution. It helps me. [nced cloud][1] [1]: https://my-ncedcloud-login.us/

Comment: Merge Replicates vs Mixed Model by gabriel.hoffman ▴ 170

For your proteomics data, your normalization is correct. I had assumed it was RNA-seq because that is what I think about most. When using…

Comment: What type of counts data to import for performing Isoform analysis in edgeR by mohammedtoufiq91 ▴ 10

@gordonsmyth I will re-run Salmon with the --numGibbsSamples=50 option. Thank you.

Comment: Differential Expression Genes as Independent Variables by Gordon Smyth 52k

Such an analysis cannot be done in limma. Sorry, I cannot tell you how to do it or even whether it is possible.

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Comment: What type of counts data to import for performing Isoform analysis in edgeR

Answer: What type of counts data to import for performing Isoform analysis in edgeR

Transcript-level differential expression using DESeq2

Comment: What type of counts data to import for performing Isoform analysis in edgeR

Answer: What type of counts data to import for performing Isoform analysis in edgeR

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