Biostar Glmlrt()

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edgeR glmLRT() multiple factor design multiple testing correction

updated 8.2 years ago by Aaron Lun ★ 28k • written 8.2 years ago by Ekarl2 ▴ 80

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edger glmfit glmlrt()

updated 7.4 years ago by Aaron Lun ★ 28k • written 7.4 years ago by cadeans • 0

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2.9k

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edger contrast covariate glmlrt()

5.9 years ago Jeff Skinner • 0

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2.8k

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edger rnaseq glmlrt()

updated 8.0 years ago by James W. MacDonald 62k • written 8.0 years ago by MBWatson • 0

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2.2k

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edger differential gene expression glmlrt()

6.3 years ago simarsidhu25 • 0

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1.6k

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edger glmlrt() differential expression design and contrast matrix

updated 7.7 years ago by Gordon Smyth 47k • written 7.7 years ago by carlgdeboer • 0

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1.3k

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EdgeR glmlrt() ql f-test

6.4 years ago • updated 5.7 years ago elineverbon ▴ 20

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1.0k

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edger design matrix glmlrt() glmQFTest() paired design

4.4 years ago oakhamwolf • 0

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848

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edger differential gene expression glmlrt()

6.3 years ago • updated 6.2 years ago simarsidhu25 • 0

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Answer: Time-course, comparison of two groups by Gordon Smyth 47k

edgeR allows any number of explanatory factors, so you can have time-series for any number of treatments. If you have replicates, then I w…

Comment: different number of DEG because of outliers by Pedro Baldoni ▴ 30

The function `catchKallisto` in edgeR reads in the output from kallisto and estimates the mapping ambiguity overdispersion similarly

Comment: How to compute(calculate) rlog and vst provided from DESeq2 by tstpp • 0

Thank you for your kind reply! I try to understand them.

Answer: DESeqDataSetFromMatrix NA values by ATpoint ★ 2.3k

You have NAs in your matrix, simple as that. The check that runs internally is really just a `any(is.na(cts))`. Your check `is.numeric()` i…

Comment: How to compute(calculate) rlog and vst provided from DESeq2 by Wolfgang Huber 13k

FWIW, you can also search all of Bioconductor code via https://code.bioconductor.org e.g. https://code.bioconductor.org/search/search?q=vst

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C: deseq2 normalized data with heatmap

A: deseq2 normalized data with heatmap

Postdoc at EMBL: spatial and single-cell computational biology for precision oncology, based in Heidelberg, Germany

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