Bioconductor Gage package

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gage package gage

7.1 years ago melkile26 • 0

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gage gage package gene expression matrix gene set analysis

7.2 years ago atakanekiz ▴ 30

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3.3k

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gage package error

updated 7.3 years ago by James W. MacDonald 68k • written 7.3 years ago by Miskey, Csaba ▴ 20

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gage gage package pathview rna-seq

updated 3.5 years ago by Helen • 0 • written 7.6 years ago by tarun2 • 0

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kegg geneset genelist gage package

updated 8.1 years ago by Gordon Smyth 53k • written 8.1 years ago by sup230 ▴ 30

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gage package deseq2

8.1 years ago sup230 ▴ 30

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gage gage package

updated 8.8 years ago by Luo Weijun ★ 1.6k • written 8.9 years ago by Michael • 0

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R gage package rnaseq pathview

9.1 years ago joanito.liberti • 0

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gage package path.ids RNA-Seq

9.1 years ago rl1385 • 0

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t-test GAGE package Kolmogorov-Smirnov test Gene-Set enrichment

9.2 years ago smt8n • 0

10 results • Page 1 of 1

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Answer: Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg? by Michael Love 43k

I'm not familiar with this usage, or code here ``` normFactors <- exp(-1 * offst(set2)) ``` In the RNA-seq gene-level workflow, we …

Answer: Which of apeglm and ashr may be more appropriate for pseudobulked DESeq2 analysi by Michael Love 43k

> apeglm appears much more aggressive in shrinkage, pushing many genes toward logFC = 0 > ashr maintains a gradient of shrinkage val…

Comment: voomLmFit fitted log-CPM values by Gordon Smyth 53k

The fitted values are on the log2CPM scale. I would have told you if they were not! I think you may be getting confused by the differences…

Comment: voomLmFit fitted log-CPM values by Lina ▴ 10

Is the output from fitted(v) in the log2 CPM scale? or CPM scale?

Answer: voomLmFit fitted log-CPM values by Gordon Smyth 53k

Fitted values are obtained from limma MArrayLM objects by ``` fitted(v) ```

Votes

A: How barcode-plot enrichment is calculated?

Answer: ROAST compare results with complex design

How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?

Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea

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