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methylationArrayAnalysis minfiData minfi MethylationArrayData MethylationArray

written 13 months ago by Grace • 0

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methylationArrayAnalysis minfiData minfi MethylationArrayData MethylationArray

updated 13 months ago by James W. MacDonald 65k • written 13 months ago by Grace • 0

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RnBeads minfiData minfi EPICarray

updated 11 months ago by Basti ▴ 770 • written 11 months ago by Jitendra ▴ 10

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minfi methylation dataimport minfidata missmethyl

updated 5.6 years ago by James W. MacDonald 65k • written 5.6 years ago by moldach ▴ 20

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minfi minfidata illumina methylation dmpfinder

updated 9.6 years ago by James W. MacDonald 65k • written 9.6 years ago by michael.zulyniak • 0

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minfi minfidata rgl. mac os x el capitan

updated 8.0 years ago by Kasper Daniel Hansen ★ 6.5k • written 8.0 years ago by holbrookjoanna • 0

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minfidata minfi illuminahumanmethylation450k.db illuminahumanmethylation450kanno.ilmn12.hg19

9.0 years ago alejandretheodore • 0

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minfiData plotsex minfi minfiDataEPIC r

updated 3.1 years ago by suman • 0 • written 3.1 years ago by Bethan • 0

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methylclockData minfi methylclock minfidata

updated 7 weeks ago by James W. MacDonald 65k • written 7 weeks ago by sharangiiv • 0

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minfiData ChAMP

2.3 years ago behr201 • 0

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minfi minfiData MethylationArrayData

2.7 years ago ponche_de_kiwi • 0

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Comment: Differential peaks that were not identified in diffbind were identified in diseq by ATpoint ★ 4.0k

Make an MAplot. There is almost certainly an issue with normalization here given the very biased distribution of logFCs as in this Volcano.

Comment: significant difference of p-values with dream() after updating VariancePartition by gabriel.hoffman ▴ 100

See variancePartition updates for [v1.33.11](https://diseaseneurogenomics.github.io/variancePartition/news/index.html#variancepartition-133…

Comment: A ComBat-seq issue: the covariates are confounded by W. Evan Johnson ▴ 850

This is only partially confounded because there is overlap between the batches -- they both have GFP controls that can be used to remove ba…

Answer: Different number of exons in reference genome affects DEXSeq analysis by Alejandro Reyes ★ 1.9k

Likely the new annotation that you are using has more annotated isoforms, and thus the exons are splitted into more disjoint exonic bins. I…

Answer: Adding columns to DEXSeqResults object by Alejandro Reyes ★ 1.9k

I'd have a look into the match function, that could give you a mapping between the ids in the dxr1 object and your data frame of gene symbo…

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Comment: DEXSeq DEXSeqDataSet count matrix duplication

Comment: Error in champ.load(): The following specified files do not exist

Answer: Error in read.metharray(basenames = files, extended = extended, verbose = verbos

Using GRanges and IRanges to simply get all chromosome data

A: Using GRanges and IRanges to simply get all chromosome data

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