Bioconductor DesignMatrix

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subsettingdata edgeR designmatrix

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limma designmatrix

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DESeq2 designmatrix edgeR limma tidybulk

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R designmatrix edgeR limma model.matrix

18 months ago Abdul ▴ 20

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DESeq2 limma modelmatrix edgeR designmatrix

updated 2.6 years ago by Gordon Smyth 51k • written 2.7 years ago by rebecca.lea.johnston • 0

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designmatrix deseq2 DESeq2

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designmatrix RNA-seq limma

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designmatrix DifferentialExpression edgeR RNAseq

3.3 years ago nageshprabhu.k ▴ 10

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MutlipleFactors DesignMatrix edgeR

3.3 years ago Debayan ▴ 20

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edgeR pairedsamples designmatrix

3.4 years ago • updated 3.3 years ago sfidemw • 0

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deseq2 miRNASeq designmatrix Batch

updated 4.2 years ago by Michael Love 42k • written 4.2 years ago by anshulmbi • 0

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edger r differentialanalysis rnaseq designmatrix

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

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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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limma microarray designmatrix

updated 7.9 years ago by Aaron Lun ★ 28k • written 7.9 years ago by nashchem • 0

14 results • Page 1 of 1

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Comment: gds in GEOmetadb 2023-06-26 version is empty by Frederico Moraes Ferreira ▴ 100

Try axel -n 20 https://gbnci.cancer.gov/geo/GEOmetadb.sqlite.gz

Comment: Most enriched pathway is not expressed when modifying universe parameter by James W. MacDonald 66k

The default for `enrichGO` is to subset to those with a p-value<0.05. You don't adjust that default argument, so you shouldn't have any GO …

Answer: In a 3 group DEG analysis with three batches, can I use 1 group in all three bat by Michael Love 42k

You can compare A and C thanks to the sharing of samples from B across 1, 2 and 3.

Comment: Most enriched pathway is not expressed when modifying universe parameter by adripel • 0

In the enrichGO results we have significant and non-significant enriched terms that are displayed. So why would an enriched term (significa…

Answer: Design formula, numeric contrast, and lfcshrink in deseq2 by Michael Love 42k

For questions about how to construct the correct contrasts correspond to particular hypotheses, I recommend consulting with a local statist…

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Comment: Most enriched pathway is not expressed when modifying universe parameter

Time-course, comparison of two groups

Answer: Behaviour of featureCounts when quantifying multi-mapping reads

Answer: GESA with certain gene list returns no result with human genom, but many result

Answer: Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`

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