Bioconductor GlmLRT()

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1.8k

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edger design matrix glmlrt() glmQFTest() paired design

7.2 years ago oakhamwolf • 0

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2.8k

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EdgeR glmlrt() ql f-test

9.2 years ago • updated 8.5 years ago elineverbon ▴ 20

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4.4k

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edger contrast covariate glmlrt()

8.8 years ago Jeff Skinner • 0

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1.7k

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edger differential gene expression glmlrt()

9.1 years ago simarsidhu25 • 0

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3.6k

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edger differential gene expression glmlrt()

9.1 years ago simarsidhu25 • 0

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4.5k

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edger glmfit glmlrt()

updated 10.2 years ago by Aaron Lun ★ 29k • written 10.2 years ago by cadeans • 0

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2.5k

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edger glmlrt() differential expression design and contrast matrix

updated 10.6 years ago by Gordon Smyth 53k • written 10.6 years ago by carlgdeboer • 0

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4.8k

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edger rnaseq glmlrt()

updated 10.8 years ago by James W. MacDonald 68k • written 10.8 years ago by MBWatson • 0

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edgeR glmLRT() multiple factor design multiple testing correction

updated 11.0 years ago by Aaron Lun ★ 29k • written 11.0 years ago by Ekarl2 ▴ 80

9 results • Page 1 of 1

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Answer: Confounded design, batch effect correction (edgeR) by nig.httopss • 0

To perform gene matching accurately, you should use the formula ~0 + Group + Batch in the design matrix to better manage sample groups. Sin…

Comment: Clarification on counting in Rsubread (featureCounts) by Gordon Smyth 53k

Have you told featureCounts to do strand-specific counting? As pointed out by Frances Turner, you can lose reads if they overlap the gene …

Answer: Clarification on counting in Rsubread (featureCounts) by Frances Turner ▴ 10

You should look at the summary files produced by feature counts. This gives a breakdown of what happened to reads that were not assigned. Y…

Comment: Incosistencies in buildSNNGraph() function by ATpoint ★ 5.0k

Just played with this a bit and I think it comes down to not having a fixed seed before running the leiden thingy. Same goes for PCA and UM…

Answer: Incosistencies in buildSNNGraph() function by Aaron Lun ★ 29k

The most obvious thing that comes to mind is the RNG seed. `cluster_leiden()` does some random number generation, somewhere deep in the **i…

Votes

Answer: Clarification on counting in Rsubread (featureCounts)

C: RNA-Seq analysis with Limma/edgeR, time course experiment, aberrant results

A: Conversion from counts to FPKM

Answer: Incosistencies in buildSNNGraph() function

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Great Question to fl ▴ 20

Popular Question to Lluís Revilla Sancho ▴ 760