Bioconductor Interaction

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693

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DESeq2 interaction coefficient LinearModel RNASeq

updated 17 months ago by Michael Love 41k • written 17 months ago by Pedro Milanez-Almeida ▴ 10

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655

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interaction DESeq2

updated 21 months ago by swbarnes2 ★ 1.3k • written 21 months ago by Tait • 0

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3.3k

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DifferentialExpression contrasts interaction DESeq2

written 24 months ago by Nicole ▴ 10

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791

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DESeq2 interaction pairwise

2.7 years ago Lucas • 0

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6.0k

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LRT DESeq2 interaction

updated 3.1 years ago by Kevin Blighe ★ 3.9k • written 3.1 years ago by annamariabugaj ▴ 10

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1.1k

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limma interaction

3.7 years ago Sindre ▴ 110

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1.0k

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DESeq2 interaction differential expression

updated 3.8 years ago by Michael Love 41k • written 3.8 years ago by charles.foster ▴ 160

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822

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mircomb mrna mirna degs interaction

3.8 years ago andreia ▴ 10

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1.0k

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deseq2 interaction model

updated 3.9 years ago by Michael Love 41k • written 3.9 years ago by aec ▴ 90

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810

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graphite interaction

updated 4.0 years ago by gabriele.sales ▴ 100 • written 4.0 years ago by emisecherre • 0

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1.4k

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deseq2 interaction

updated 4.2 years ago by sebastian.lobentanzer ▴ 50 • written 4.2 years ago by ktrns • 0

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1.2k

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random effects interaction limma rna-seq

4.9 years ago flippy23 • 0

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732

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edger deseq2 interaction design matrix

updated 5.2 years ago by James W. MacDonald 65k • written 5.2 years ago by Assa Yeroslaviz ★ 1.5k

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977

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DEXSeq interaction

5.3 years ago zhenzuo2 • 0

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853

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edge differential gene expression timecourse interaction

5.7 years ago rubi ▴ 110

15 results • Page 1 of 1

Recent ...

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Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k

Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…

Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0

Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…

Comment: PCA plot suggestions by JKim • 0

cross post: https://www.biostars.org/p/9593486/

Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k

You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…

Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by James W. MacDonald 65k

You will need to show some reproducible code for anybody to track this down. Please note that `DESeq2` has been used by thousands of people…

Votes

Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2

Answer: Use of negative binomial model for exponential decay rate estimation using DESeq

C: null model and DEXSeqDataSet object in DEXSEQ

A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?

A: How to explain how DESeq2 works to someone with zero bioinformatics background?

Awards • All

Scholar to James W. MacDonald 65k

Supporter to JKim • 0