Bioconductor DesignMatrix

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R designmatrix edgeR limma model.matrix

17 months ago Abdul ▴ 20

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Limma designMatrix

updated 5.9 years ago by Aaron Lun ★ 28k • written 5.9 years ago by Keifa ▴ 10

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DESeq2 designmatrix edgeR limma tidybulk

updated 15 months ago by Michael Love 42k • written 15 months ago by aditya.m ▴ 10

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limma microarray designmatrix

updated 7.8 years ago by Aaron Lun ★ 28k • written 7.8 years ago by nashchem • 0

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954

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MutlipleFactors DesignMatrix edgeR

3.3 years ago Debayan ▴ 20

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DESeq2 limma modelmatrix edgeR designmatrix

updated 2.6 years ago by Gordon Smyth 50k • written 2.6 years ago by rebecca.lea.johnston • 0

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subsettingdata edgeR designmatrix

updated 4 weeks ago by Gordon Smyth 50k • written 4 weeks ago by prity6459 • 0

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designmatrix deseq2 DESeq2

updated 2.6 years ago by swbarnes2 ★ 1.4k • written 2.6 years ago by OST • 0

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918

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edgeR pairedsamples designmatrix

3.3 years ago sfidemw • 0

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designmatrix RNA-seq limma

updated 3.1 years ago by Gordon Smyth 50k • written 3.2 years ago by athief ▴ 20

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edger r differentialanalysis rnaseq designmatrix

updated 5.0 years ago by Aaron Lun ★ 28k • written 5.1 years ago by Beginner ▴ 60

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695

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deseq2 miRNASeq designmatrix Batch

updated 4.1 years ago by Michael Love 42k • written 4.1 years ago by anshulmbi • 0

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187

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limma designmatrix

updated 6 weeks ago by Gordon Smyth 50k • written 6 weeks ago by avery • 0

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designmatrix DifferentialExpression edgeR RNAseq

3.2 years ago nageshprabhu.k ▴ 10

14 results • Page 1 of 1

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Answer: all variables in design formula must be columns in colData (Deseq2) error by ATpoint ★ 4.1k

Your code is poorly readable. Suggest you select and then highlight with markdown using the `10101` button. Generally, colData(dds) must…

Answer: Subsetting RNAseq data | voomaByGroup() by Gordon Smyth 50k

Judging from your MDS plot, cell types 1 and 2 look radically different, so it would make perfect sense to analyse them separately. There's…

Answer: Numerical differences in DESeq2 output depending on different design matrix cons by Michael Love 42k

Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.

Answer: DESeq2- Mysterious interaction suppresses DEGs by Michael Love 42k

Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…

Comment: Ensembl plants at annotationHub? by Daniele • 0

Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!

Votes

Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")

Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools

Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa

Rsubread counting peaks ATACseq

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