Bioconductor GOfuncR

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GOfuncR

updated 19 months ago by Steffi Grote ▴ 10 • written 2.0 years ago by Marek Gierlinski ▴ 30

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analysis R GOfuncR

updated 2.2 years ago by Lluís Revilla Sancho ▴ 760 • written 2.2 years ago by Eliza • 0

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GO.db GOfuncR GO GOSim goProfiles

updated 2.9 years ago by Basti ▴ 780 • written 2.9 years ago by yeluo • 0

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GOfuncR

3.9 years ago • updated 3.2 years ago capricygcapricyg ▴ 10

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GOfuncR plot_anno_scores plot_stats

updated 7.0 years ago by steffi_grote • 0 • written 7.0 years ago by rbenel ▴ 50

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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) ```

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A: How barcode-plot enrichment is calculated?

Answer: ROAST compare results with complex design

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