Bioconductor DNA Methylation

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1.3k

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minfi cell proportion estimateCellCounts DNA Methylation

5.5 years ago grayapply2009 • 0

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2.9k

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normalization DNA methylation WGCNA

updated 6.2 years ago by Peter Langfelder ★ 3.0k • written 6.2 years ago by enora.fremy • 0

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1.4k

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medips medip-seq dna methylation dmr analysis

updated 6.8 years ago by Lukas Chavez ▴ 570 • written 6.8 years ago by mtefit • 0

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2.1k

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R gdc rna-seq dna methylation

updated 6.9 years ago by Sean Davis 21k • written 6.9 years ago by RichardJActon ▴ 50

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1.8k

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minfi normalization outliers dna methylation densityplot

7.1 years ago peter.fransquet • 0

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993

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differential variability dna methylation iEVORA DVP

7.4 years ago poojitha.stemcell ▴ 10

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1.3k

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rnbeads methylation methylationepic dna methylation

7.6 years ago gabrielrfries • 0

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1.4k

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dna methylation biseq

updated 7.7 years ago by Gordon Smyth 53k • written 7.7 years ago by ahmad.moousavi • 0

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2.4k

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tcgabiolinks dna methylation

updated 7.8 years ago by Marcel Ramos 700 • written 7.8 years ago by michaelwxf2012 • 0

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2.4k

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dna methylation illimina 450k methylation beta M significance

updated 8.0 years ago by James W. MacDonald 68k • written 8.0 years ago by skids121 • 0

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1.6k

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CNV minfi preprocessing dna methylation

8.5 years ago Thomas • 0

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1.3k

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microarray HM450 dna methylation cohcap

updated 8.6 years ago by James W. MacDonald 68k • written 8.6 years ago by poojitha.stemcell ▴ 10

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1.4k

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minfi bumphunter DNA methylation illumina450k

updated 9.2 years ago by James W. MacDonald 68k • written 9.2 years ago by fleur_p90 • 0

13 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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