Bioconductor Merge data frames

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deseq2 deseq merge data frames cbind s4vectors

updated 7.9 years ago by Michael Love 43k • written 7.9 years ago by kirannbishwa01 ▴ 20

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merge merge data frames

updated 8.2 years ago by Haiying.Kong ▴ 110 • written 8.2 years ago by shadhiksk • 0

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bioconductor merge data frames combine biocgenerics

9.8 years ago • updated 22 months ago Konstantinos Yeles ▴ 90

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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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