Showing : methylationArrayAnalysis • reset
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When doing differential methylation using the sesame package, seems to only go one way
methylation sesame methylationArrayAnalysis
updated 3 months ago by ▴ 20 • written 3 months ago by ▴ 10
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2
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509
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In the sesame package, what does the estimate output mean from testEnrichment()
MethylationArray methylation sesame methylationArrayAnalysis
3 months ago ramiro.barrantes ▴ 10
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1
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301
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Annotating DMRs
MethylationArray MethylationArrayData methylationArrayAnalysis
updated 3 months ago by 67k • written 3 months ago by ▴ 10
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1
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492
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ChAMP analysis Error: Meth Matrix and UnMeth Matrix seems not paried correctly AND incomplete final line
MethylationArray methylationArrayAnalysis ChAMP
updated 24 days ago by • 0 • written 5 months ago by • 0
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7
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1.4k
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Methylation Analysis experiment design using Limma
DNAMethylation limma methylationArrayAnalysis
8 months ago hortense96 • 0
1
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1
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1.0k
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Need Advice: Issue with ChAMP Analysis - Meth and UnMeth Matrix Pairing Error
MethylationArray methylationArrayAnalysis ChAMP
updated 10 months ago by 67k • written 10 months ago by • 0
1
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4
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1.0k
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EPIC or EPICv2 demo data of brain samples. FlowSorted.DLPFC.EPIC Availability?
DNAMethylation MethylationArray methylationArrayAnalysis illumina
10 months ago mikat • 0
2
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4
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1.2k
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Correct the batch effect in methylation analysis in R
BatchEffect limma methylationArrayAnalysis
updated 12 months ago by 52k • written 12 months ago by • 0
3
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6
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1.2k
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Methylation data analysis
MethylationArrayData methylationArrayAnalysis
13 months ago aldea85 • 0
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1
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1.1k
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EPIC v2 demo data from blood samples
MethylationArray methylationArrayAnalysis
updated 14 months ago by 67k • written 14 months ago by • 0
1
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3
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882
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Merging Methylation data (M-values) with phenotypic data
MethylationArrayData methylationArrayAnalysis
updated 16 months ago by 67k • written 16 months ago by • 0
0
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1
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3.5k
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Warning messages in detecting P-values
minfiDataEPIC methylationArrayAnalysis
updated 17 months ago by ★ 4.6k • written 17 months ago by ▴ 10
1
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2
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870
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edgeR, RRBS Library size preparation
RRBSdata edgeR methylationArrayAnalysis
17 months ago Krzysztof • 0
1
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2
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1.0k
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How to perform a methylation analyisis from m values
MethylationArrayData methylationArrayAnalysis
18 months ago Irene • 0
1
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1
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788
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urgent error for producing table of topGO() annotated DMPs methylation
methylationArrayAnalysis topGO missMethyl MethylationArrayData MethylationArray
updated 19 months ago by ▴ 40 • written 20 months ago by • 0
2
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6
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1.5k
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cpg.annotate() in DMRcate error
DNAMethylation methylationArrayAnalysis DMRcate MethylationArrayData MethylationArray
updated 20 months ago by ▴ 200 • written 20 months ago by • 0
0
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2
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1.4k
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Error in loading file using champ.load() from ChAMP package
champ.load epicarray ChAMP methylationArrayAnalysis
20 months ago • updated 19 months ago arisarkar88 ▴ 40
0
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1
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746
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LmFit error in EPIC methylation array analysis, Minfi
methylationArrayAnalysis minfi MethylationArrayData minfiDataEPIC MethylationArray
updated 20 months ago by 52k • written 21 months ago by • 0
0
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1
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867
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specifying comparison of interest in the minfi Bumhunter function
limma bumphunter methylationArrayAnalysis minfi
updated 21 months ago by 67k • written 21 months ago by • 0
5
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1
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1.8k
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Support for new Illumina human methylation EPIC array v2
human methylationArrayAnalysis
updated 11 months ago by • 0 • written 21 months ago by ▴ 80
0
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4
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1.5k
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Sex estimation problems in [estimateCellCounts]: methylation arrays
methylationArrayAnalysis minfiData minfi MethylationArrayData MethylationArray
updated 21 months ago by 67k • written 21 months ago by • 0
0
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5
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1.7k
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minfi error read.metharray.exp
methylationArrayAnalysis minfiData minfi MethylationArrayData MethylationArray
written 21 months ago by • 0
0
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1
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856
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Job: 'Omics data analyst for HPCBio, University of Illinois
SingleCell rnaseq methylationArrayAnalysis Spatial
written 2.0 years ago by ★ 2.0k
0
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3
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3.8k
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Error: BiocParallel errors 1 remote errors, element index: 1 506 unevaluated and other errors first remote error:
methylationArrayAnalysis
updated 17 months ago by • 0 • written 2.2 years ago by • 0
0
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7
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3.2k
views
ERROR happens when install "DSS" package
methylationArrayAnalysis ChAMP DMP DSS
updated 2.2 years ago by 67k • written 2.6 years ago by • 0
0
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0
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914
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filtering options in RnBeads for array data
Epigenetics RnBeads MethylationArrayData methylationArrayAnalysis
2.7 years ago Jitendra ▴ 10
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0
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1.2k
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getsex function error.
QualityControl methylationArrayAnalysis
2.9 years ago zusman • 0
2
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4
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1.5k
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How to get methylation data in count data format from "Infinium MethylationEPIC BeadChips (Illumina)" idat files
methylationArrayAnalysis illuminaio beadarray DSS bsseqData
2.9 years ago Jojo • 0
0
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6
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4.0k
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Merge problems in R
methylationArrayAnalysis ChAMP MethylationArrayData
3.4 years ago FWNL15 • 0
0
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2
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1.2k
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Limma experiment design and making contrasts
limma methylationArrayAnalysis
3.7 years ago Kesava • 0
1
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8
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1.7k
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EPIC array single replicate pipeline?
minfi methylationArrayAnalysis
3.7 years ago chay • 0
0
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2
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1.6k
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champ.SVD() : Error in while (step == 0) { : missing value where TRUE/FALSE needed
methylationArrayAnalysis EPICarray ChAMP Champ.SVD
3.7 years ago arisarkar88 ▴ 40
0
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2
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1.1k
views
Error myDMP not found
Illumina methylationArrayAnalysis ChAMPdata ChAMP
3.9 years ago sissialva21 • 0
2
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7
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3.0k
views
Blood cell composition adjustment in methylation EPIC array: ChAMP
MethylationArray methylationArrayAnalysis ChAMP
updated 14 months ago by • 0 • written 4.0 years ago by ▴ 20
1
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1
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1.4k
views
Error in read.metharray(basenames = files, extended = extended, verbose = verbose, : The following specified files do not exist:201172580052_R02C…
ArrayExpress methylationArrayAnalysis
updated 4.1 years ago by 67k • written 4.1 years ago by • 0
35 results • Page 1 of 1
Recent ...
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Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by xiaofeiwang198266 • 0
Thanks for your reply!
Votes
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
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