Bioconductor Variance

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5.8k

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supervised edgeR variance RNASeq heatmaps

updated 2.2 years ago by Gordon Smyth 52k • written 2.3 years ago by mohammedtoufiq91 ▴ 10

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1.5k

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limma treatment variance

updated 5.3 years ago by Gordon Smyth 52k • written 5.3 years ago by ML18 ▴ 10

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1.2k

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deseq2 vst variance

updated 5.9 years ago by Michael Love 43k • written 5.9 years ago by Bitao Qiu • 0

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1.8k

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variance formula expression

updated 6.3 years ago by mikhael.manurung ▴ 280 • written 6.3 years ago by rina ▴ 30

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1.2k

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deseq2 variance genes

updated 7.4 years ago by Michael Love 43k • written 7.4 years ago by hs.lansdell ▴ 20

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7.7k

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deseq2 counts DESeqtransform variance deviation

updated 7.5 years ago by Michael Love 43k • written 7.5 years ago by Casper van Mourik • 0

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1.9k

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deseq2 variance lrt differential gene expression

updated 8.1 years ago by Ryan C. Thompson ★ 7.9k • written 8.1 years ago by rclaire ▴ 20

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2.2k

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pca variance deseq2 gene_id

updated 8.9 years ago by Michael Love 43k • written 8.9 years ago by NMostajo ▴ 10

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2.6k

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limma arrayWeights variance sampleQuality microarray

updated 9.5 years ago by Ryan C. Thompson ★ 7.9k • written 9.6 years ago by svlachavas ▴ 840

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Comment: Differing results with DESeq2 by JKim • 0

I think it would be more straightforward if you use cellmeans model. Have a look at [A guide to creating design matrices for gene expressio…

Answer: CluserProfiler message "No gene can be mapped" by James W. MacDonald 68k

Your gene IDs are things like this: `Mpyr-NLJ1B.v3.hap1.scaffold1.g290550`, and the genes in your term2gene table are things like this: `Mp…

Answer: RNA-seq input to GRaNIE by James W. MacDonald 68k

This is [covered in the vignette.][1] [1]: https://bioconductor.org/packages/release/bioc/vignettes/GRaNIE/inst/doc/GRaNIE_packageDe…

Answer: Help using reduceSimMatrix with a custom annotation by sergisayolspuig ▴ 80

Hi there, `reduceSimMatrix()` expects a "GOALL" keytype in the OrgDb object when called with `children=TRUE` (which is the default for thi…

Answer: Analyzing TnSeq data with DESeq2 by cold.wolverine.arku • 0

That's a great use case of DESeq2! Even though it's not specifically tailored for TnSeq data, your approach to normalize and run explorator…

Votes

A: Unbalanced experiment with multiple samples from each patient.

A: Understanding contrasts limma

Answer: ROAST for small sets

A: conceptual question about FDR, FDR adjusted p-value and q-value

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