Showing : methylationArrayAnalysis • reset
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urgent error for producing table of topGO() annotated DMPs methylation
methylationArrayAnalysis topGO missMethyl MethylationArrayData MethylationArray
updated 4 weeks ago by ▴ 40 • written 4 weeks ago by • 0
2
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6
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334
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cpg.annotate() in DMRcate error
DNAMethylation methylationArrayAnalysis DMRcate MethylationArrayData MethylationArray
updated 5 weeks ago by ▴ 140 • written 5 weeks ago by • 0
0
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2
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185
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Error in loading file using champ.load() from ChAMP package
champ.load epicarray ChAMP methylationArrayAnalysis
5 weeks ago • updated 26 days ago arisarkar88 ▴ 40
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1
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119
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LmFit error in EPIC methylation array analysis, Minfi
methylationArrayAnalysis minfi MethylationArrayData minfiDataEPIC MethylationArray
updated 8 weeks ago by 47k • written 8 weeks ago by • 0
0
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1
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149
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specifying comparison of interest in the minfi Bumhunter function
limma bumphunter methylationArrayAnalysis minfi
updated 11 weeks ago by 63k • written 11 weeks ago by • 0
2
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0
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246
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Support for new Illumina human methylation EPIC array v2
human methylationArrayAnalysis
12 weeks ago jenniewoo ▴ 40
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4
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207
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Sex estimation problems in [estimateCellCounts]: methylation arrays
methylationArrayAnalysis minfiData minfi MethylationArrayData MethylationArray
updated 11 weeks ago by 63k • written 12 weeks ago by • 0
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5
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297
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minfi error read.metharray.exp
methylationArrayAnalysis minfiData minfi MethylationArrayData MethylationArray
written 12 weeks ago by • 0
0
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1
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262
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Job: 'Omics data analyst for HPCBio, University of Illinois
SingleCell rnaseq methylationArrayAnalysis Spatial
written 5 months ago by ★ 2.0k
0
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2
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847
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Error: BiocParallel errors 1 remote errors, element index: 1 506 unevaluated and other errors first remote error:
methylationArrayAnalysis
7 months ago shuangshuang • 0
0
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7
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1.5k
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ERROR happens when install "DSS" package
methylationArrayAnalysis ChAMP DMP DSS
updated 7 months ago by 63k • written 12 months ago by • 0
0
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0
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373
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filtering options in RnBeads for array data
Epigenetics RnBeads MethylationArrayData methylationArrayAnalysis
14 months ago Jitendra ▴ 10
0
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0
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339
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getsex function error.
QualityControl methylationArrayAnalysis
15 months ago zusman • 0
2
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4
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649
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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
16 months ago Jojo • 0
0
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6
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2.3k
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Merge problems in R
methylationArrayAnalysis ChAMP MethylationArrayData
22 months ago FWNL15 • 0
0
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2
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607
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Limma experiment design and making contrasts
limma methylationArrayAnalysis
2.1 years ago Kesava • 0
1
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8
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864
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EPIC array single replicate pipeline?
minfi methylationArrayAnalysis
2.2 years ago • updated 2.1 years ago chay • 0
0
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2
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861
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champ.SVD() : Error in while (step == 0) { : missing value where TRUE/FALSE needed
methylationArrayAnalysis EPICarray ChAMP Champ.SVD
2.2 years ago • updated 2.1 years ago arisarkar88 ▴ 40
0
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2
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598
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Error myDMP not found
Illumina methylationArrayAnalysis ChAMPdata ChAMP
2.3 years ago sissialva21 • 0
2
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6
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1.6k
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Blood cell composition adjustment in methylation EPIC array: ChAMP
MethylationArray methylationArrayAnalysis ChAMP
updated 14 months ago by • 0 • written 2.5 years ago by ▴ 20
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1
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613
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Error in read.metharray(basenames = files, extended = extended, verbose = verbose, : The following specified files do not exist:201172580052_R02C…
ArrayExpress methylationArrayAnalysis
updated 2.6 years ago by 63k • written 2.6 years ago by • 0
21 results • Page 1 of 1
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Comment: Question on constructing design matrix and defining contrasts for analysis by mohammedtoufiq91 ▴ 10
Sure, noted.
Comment: Question on constructing design matrix and defining contrasts for analysis by mohammedtoufiq91 ▴ 10
@gordonsmyth Yes, I realized while re-running through the WGCNA workflow and forget to account for the paired experiment. For general gene …
Comment: Question on constructing design matrix and defining contrasts for analysis by Gordon Smyth 47k
PS. Just as aside, using `dput` to show a data.frame is unnecessary overkill. Just typing `targetsframe` at the prompt would do the job.
Comment: Question on constructing design matrix and defining contrasts for analysis by Gordon Smyth 47k
> Basically, I want to create a design matrix and binarize by 0 and 1 to be used in WGCNA analysis to compare module between/within groups …
Comment: SummarizedExperiment is now warning on attach about `read_block` namespace confl by ansleyharralson • 0
Any estimate on when DelayedArray 0.26.3 will be released for macOS Binary (arm64)? Latest is still 0.26.02 best I can tell.
Votes
WGCNA coupled with differential expression analysis: question about baseline module detection
WGCNA with paired samples
Comment: Question on constructing design matrix and defining contrasts for analysis
Comment: Question on constructing design matrix and defining contrasts for analysis
Answer: Question on constructing design matrix and defining contrasts for analysis
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