Showing : methylationarrayanalysis • reset
2
votes
7
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2.4k
views
Blood cell composition adjustment in methylation EPIC array: ChAMP
MethylationArray methylationArrayAnalysis ChAMP
updated 6 months ago by • 0 • written 3.4 years ago by ▴ 20
1
vote
3
replies
522
views
Merging Methylation data (M-values) with phenotypic data
MethylationArrayData methylationArrayAnalysis
updated 8 months ago by 65k • written 8 months ago by • 0
0
votes
2
replies
875
views
Error myDMP not found
Illumina methylationArrayAnalysis ChAMPdata ChAMP
3.3 years ago sissialva21 • 0
1
vote
1
reply
1.1k
views
Error in read.metharray(basenames = files, extended = extended, verbose = verbose, : The following specified files do not exist:201172580052_R02C…
ArrayExpress methylationArrayAnalysis
updated 3.5 years ago by 65k • written 3.5 years ago by • 0
1
vote
8
replies
1.4k
views
EPIC array single replicate pipeline?
minfi methylationArrayAnalysis
3.1 years ago chay • 0
1
vote
1
reply
291
views
Need Advice: Issue with ChAMP Analysis - Meth and UnMeth Matrix Pairing Error
MethylationArray methylationArrayAnalysis ChAMP
updated 10 weeks ago by 65k • written 10 weeks ago by • 0
0
votes
2
replies
1.0k
views
Error in loading file using champ.load() from ChAMP package
champ.load epicarray ChAMP methylationArrayAnalysis
12 months ago arisarkar88 ▴ 40
0
votes
1
reply
734
views
EPIC v2 demo data from blood samples
MethylationArray methylationArrayAnalysis
updated 7 months ago by 65k • written 7 months ago by • 0
0
votes
1
reply
2.5k
views
Warning messages in detecting P-values
minfiDataEPIC methylationArrayAnalysis
updated 9 months ago by ★ 4.1k • written 9 months ago by ▴ 10
0
votes
5
replies
1.2k
views
minfi error read.metharray.exp
methylationArrayAnalysis minfiData minfi MethylationArrayData MethylationArray
written 14 months ago by • 0
0
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7
replies
302
views
Methylation Analysis experiment design using Limma
DNAMethylation limma methylationArrayAnalysis
16 days ago • updated 10 days ago hortense96 • 0
0
votes
1
reply
542
views
LmFit error in EPIC methylation array analysis, Minfi
methylationArrayAnalysis minfi MethylationArrayData minfiDataEPIC MethylationArray
updated 13 months ago by 50k • written 13 months ago by • 0
0
votes
4
replies
1.0k
views
Sex estimation problems in [estimateCellCounts]: methylation arrays
methylationArrayAnalysis minfiData minfi MethylationArrayData MethylationArray
updated 14 months ago by 65k • written 14 months ago by • 0
1
vote
2
replies
586
views
edgeR, RRBS Library size preparation
RRBSdata edgeR methylationArrayAnalysis
10 months ago • updated 9 months ago Krzysztof • 0
1
vote
2
replies
642
views
How to perform a methylation analyisis from m values
MethylationArrayData methylationArrayAnalysis
11 months ago • updated 10 months ago Irene • 0
2
votes
6
replies
1.1k
views
cpg.annotate() in DMRcate error
DNAMethylation methylationArrayAnalysis DMRcate MethylationArrayData MethylationArray
updated 12 months ago by ▴ 180 • written 12 months ago by • 0
0
votes
7
replies
2.6k
views
ERROR happens when install "DSS" package
methylationArrayAnalysis ChAMP DMP DSS
updated 18 months ago by 65k • written 24 months ago by • 0
0
votes
3
replies
2.8k
views
Error: BiocParallel errors 1 remote errors, element index: 1 506 unevaluated and other errors first remote error:
methylationArrayAnalysis
updated 9 months ago by • 0 • written 18 months ago by • 0
2
votes
4
replies
629
views
Correct the batch effect in methylation analysis in R
BatchEffect limma methylationArrayAnalysis
updated 4 months ago by 50k • written 4 months ago by • 0
3
votes
6
replies
672
views
Methylation data analysis
MethylationArrayData methylationArrayAnalysis
5 months ago aldea85 • 0
0
votes
1
reply
607
views
specifying comparison of interest in the minfi Bumhunter function
limma bumphunter methylationArrayAnalysis minfi
updated 13 months ago by 65k • written 13 months ago by • 0
1
vote
1
reply
562
views
urgent error for producing table of topGO() annotated DMPs methylation
methylationArrayAnalysis topGO missMethyl MethylationArrayData MethylationArray
updated 12 months ago by ▴ 40 • written 12 months ago by • 0
0
votes
0
replies
719
views
filtering options in RnBeads for array data
Epigenetics RnBeads MethylationArrayData methylationArrayAnalysis
2.1 years ago Jitendra ▴ 10
5
votes
1
reply
1.4k
views
Support for new Illumina human methylation EPIC array v2
human methylationArrayAnalysis
updated 3 months ago by • 0 • written 14 months ago by ▴ 70
2
votes
4
replies
1.3k
views
How to get methylation data in count data format from "Infinium MethylationEPIC BeadChips (Illumina)" idat files
methylationArrayAnalysis illuminaio beadarray DSS bsseqData
2.2 years ago Jojo • 0
0
votes
0
replies
928
views
getsex function error.
QualityControl methylationArrayAnalysis
2.2 years ago zusman • 0
1
vote
4
replies
465
views
EPIC or EPICv2 demo data of brain samples. FlowSorted.DLPFC.EPIC Availability?
DNAMethylation MethylationArray methylationArrayAnalysis illumina
12 weeks ago mikat • 0
0
votes
2
replies
1.4k
views
champ.SVD() : Error in while (step == 0) { : missing value where TRUE/FALSE needed
methylationArrayAnalysis EPICarray ChAMP Champ.SVD
3.1 years ago arisarkar88 ▴ 40
0
votes
1
reply
662
views
Job: 'Omics data analyst for HPCBio, University of Illinois
SingleCell rnaseq methylationArrayAnalysis Spatial
written 17 months ago by ★ 2.0k
0
votes
2
replies
957
views
Limma experiment design and making contrasts
limma methylationArrayAnalysis
3.1 years ago Kesava • 0
0
votes
6
replies
3.4k
views
Merge problems in R
methylationArrayAnalysis ChAMP MethylationArrayData
2.8 years ago FWNL15 • 0
31 results • Page 1 of 1
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Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0
Thank you Tim, this is a great help in getting me started!
Comment: Too many significant genes when integrating gtex and tcga by Michael Love 41k
Yes, this was one of the aspects we highlighted in the 2014 paper, and it's also in the workflow. Check these places first. Also take a st…
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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