Bioconductor Dna methylation

Showing : dna methylation • reset

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1.4k

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minfi cell proportion estimateCellCounts DNA Methylation

5.9 years ago grayapply2009 • 0

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3.2k

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normalization DNA methylation WGCNA

updated 6.6 years ago by Peter Langfelder ★ 3.0k • written 6.6 years ago by enora.fremy • 0

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1.5k

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medips medip-seq dna methylation dmr analysis

updated 7.2 years ago by Lukas Chavez ▴ 570 • written 7.2 years ago by mtefit • 0

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2.4k

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R gdc rna-seq dna methylation

updated 7.3 years ago by Sean Davis 21k • written 7.3 years ago by RichardJActon ▴ 50

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2.1k

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minfi normalization outliers dna methylation densityplot

7.5 years ago peter.fransquet • 0

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1.1k

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differential variability dna methylation iEVORA DVP

7.7 years ago poojitha.stemcell ▴ 10

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1.5k

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rnbeads methylation methylationepic dna methylation

7.9 years ago gabrielrfries • 0

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1.5k

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dna methylation biseq

updated 8.1 years ago by Gordon Smyth 53k • written 8.1 years ago by ahmad.moousavi • 0

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2.6k

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tcgabiolinks dna methylation

updated 8.2 years ago by Marcel Ramos 700 • written 8.2 years ago by michaelwxf2012 • 0

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2.6k

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dna methylation illimina 450k methylation beta M significance

updated 8.3 years ago by James W. MacDonald 68k • written 8.3 years ago by skids121 • 0

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1.7k

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CNV minfi preprocessing dna methylation

8.8 years ago Thomas • 0

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1.4k

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microarray HM450 dna methylation cohcap

updated 9.0 years ago by James W. MacDonald 68k • written 9.0 years ago by poojitha.stemcell ▴ 10

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1.5k

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minfi bumphunter DNA methylation illumina450k

updated 9.6 years ago by James W. MacDonald 68k • written 9.6 years ago by fleur_p90 • 0

13 results • Page 1 of 1

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Answer: Array weights in dpcDE by Gordon Smyth 53k

The uncertainty of quantification is fully accounted for in the dpcDE() analysis, including in the computation of sample weights. Your use…

Answer: lfc shrinkage estimator in DESeq2 by Michael Love 43k

Try the vignette which has a lot of information on these type of questions.

Comment: limpa analysis advice by Gordon Smyth 53k

The DPC slope is beta1. The estimated slopes for your data look pretty low, lower than I've ever used for a real dataset. Nevertheless, as …

Comment: limpa analysis advice by SamGG ▴ 360

Thanks for your feedback and for reassuring me. :-) As you suggested, I tried dpcCN() and set the slope to 0.7 in addition to the standard…

Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by chp265 • 0

Good point, I hadn't considered the fact quantitative `time` implies a (logit-)linear response *to* time. You're correct that I haven't exp…

Votes

A: DESeq2: Is it possible to convert read counts to expression values via TPM and r

A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen

Comment: limpa analysis advice

Answer: When to use edgeR or limma

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Popular Question to julia_mcdonough • 0