Bioconductor Bumphunter

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SNP Annotation minfi bumphunter SNP Annotation minfi bumphunter

updated 11.8 years ago by Kasper Daniel Hansen ★ 6.5k • written 11.8 years ago by Elmar Tobi ▴ 30

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SNP Annotation minfi bumphunter SNP Annotation minfi bumphunter

updated 11.8 years ago by Elmar Tobi ▴ 30 • written 11.8 years ago by Kasper Daniel Hansen ★ 6.5k

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Annotation bumphunter Annotation bumphunter

updated 12.1 years ago by Kasper Daniel Hansen ★ 6.5k • written 12.1 years ago by Anne Biton ▴ 30

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minfi bumphunter minfi bumphunter

12.2 years ago Guest User ★ 13k

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genoset minfi bumphunter genoset minfi bumphunter

12.5 years ago Matthias Zilbauer ▴ 30

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bumphunter bumphunter

updated 12.6 years ago by Kasper Daniel Hansen ★ 6.5k • written 12.6 years ago by khadeeja ismail ▴ 400

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charm minfi bsseq bumphunter charm minfi bsseq bumphunter

12.8 years ago Kasper Daniel Hansen ★ 6.5k

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PROcess rtracklayer bumphunter PROcess rtracklayer bumphunter

updated 13.8 years ago by Michael Lawrence ★ 11k • written 13.8 years ago by Leonardo Collado Torres ★ 1.1k

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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

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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