Showing : methylationarrayanalysis • reset
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Mismatch between Illumina Mouse Methylation BeadChip annotation and genome browsers (UCSC/Ensembl)
methylationArrayAnalysis MethylationArrayData
updated 8 months ago by 68k • written 8 months ago by • 0
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Correlation threshold
MethylationArray methylationArrayAnalysis StatisticalMethod
8 months ago user_bioinfo • 0
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2
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672
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Conumee2 - CNV.summaryplot()
conumee CopyNumberVariation MethylationAnalysis methylationArrayAnalysis EPICv2manifest
updated 9 months ago by 68k • written 9 months ago by • 0
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2
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541
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Meffil: error in functional normalization function (Error in rg.to.mu(rg, probes))
methylationArrayAnalysis Normalization Epigenetics MethylationArrayData
10 months ago a.alkema • 0
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378
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Unable to find sample sheet file for ChAMP methylation data analysis
MethylationArray MethylationArrayData methylationArrayAnalysis
updated 10 months ago by 68k • written 10 months ago by • 0
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2.2k
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When doing differential methylation using the sesame package, seems to only go one way
methylation sesame methylationArrayAnalysis
updated 15 months ago by ▴ 20 • written 15 months ago by ▴ 10
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In the sesame package, what does the estimate output mean from testEnrichment()
MethylationArray methylation sesame methylationArrayAnalysis
15 months ago ramiro.barrantes ▴ 10
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711
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Annotating DMRs
MethylationArray MethylationArrayData methylationArrayAnalysis
updated 15 months ago by 68k • written 15 months ago by ▴ 10
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947
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ChAMP analysis Error: Meth Matrix and UnMeth Matrix seems not paried correctly AND incomplete final line
MethylationArray methylationArrayAnalysis ChAMP
updated 12 months ago by • 0 • written 17 months ago by • 0
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2.4k
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Methylation Analysis experiment design using Limma
DNAMethylation limma methylationArrayAnalysis
20 months ago hortense96 • 0
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1
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1.7k
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Need Advice: Issue with ChAMP Analysis - Meth and UnMeth Matrix Pairing Error
MethylationArray methylationArrayAnalysis ChAMP
updated 22 months ago by 68k • written 22 months ago by • 0
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4
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1.7k
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EPIC or EPICv2 demo data of brain samples. FlowSorted.DLPFC.EPIC Availability?
DNAMethylation MethylationArray methylationArrayAnalysis illumina
22 months ago mikat • 0
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4
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Correct the batch effect in methylation analysis in R
BatchEffect limma methylationArrayAnalysis
updated 2.0 years ago by 53k • written 2.0 years ago by • 0
3
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6
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1.6k
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Methylation data analysis
MethylationArrayData methylationArrayAnalysis
2.1 years ago aldea85 • 0
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1.4k
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EPIC v2 demo data from blood samples
MethylationArray methylationArrayAnalysis
updated 2.2 years ago by 68k • written 2.2 years ago by • 0
1
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3
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1.3k
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Merging Methylation data (M-values) with phenotypic data
MethylationArrayData methylationArrayAnalysis
updated 2.3 years ago by 68k • written 2.3 years ago by • 0
0
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1
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4.0k
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Warning messages in detecting P-values
minfiDataEPIC methylationArrayAnalysis
updated 2.4 years ago by ★ 5.0k • written 2.4 years ago by ▴ 20
1
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2
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1.1k
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edgeR, RRBS Library size preparation
RRBSdata edgeR methylationArrayAnalysis
2.4 years ago Krzysztof • 0
1
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2
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1.4k
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How to perform a methylation analyisis from m values
MethylationArrayData methylationArrayAnalysis
2.5 years ago Irene • 0
1
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1
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1.1k
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urgent error for producing table of topGO() annotated DMPs methylation
methylationArrayAnalysis topGO missMethyl MethylationArrayData MethylationArray
updated 2.6 years ago by ▴ 40 • written 2.6 years ago by • 0
2
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6
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2.0k
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cpg.annotate() in DMRcate error
DNAMethylation methylationArrayAnalysis DMRcate MethylationArrayData MethylationArray
updated 2.6 years ago by ▴ 230 • written 2.6 years ago by • 0
0
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2
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1.8k
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Error in loading file using champ.load() from ChAMP package
champ.load epicarray ChAMP methylationArrayAnalysis
2.7 years ago • updated 2.6 years ago arisarkar88 ▴ 40
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1.1k
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LmFit error in EPIC methylation array analysis, Minfi
methylationArrayAnalysis minfi MethylationArrayData minfiDataEPIC MethylationArray
updated 2.7 years ago by 53k • written 2.7 years ago by • 0
0
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1.1k
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specifying comparison of interest in the minfi Bumhunter function
limma bumphunter methylationArrayAnalysis minfi
updated 2.8 years ago by 68k • written 2.8 years ago by • 0
5
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2
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2.5k
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Support for new Illumina human methylation EPIC array v2
human methylationArrayAnalysis
updated 4 months ago by • 0 • written 2.8 years ago by ▴ 80
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4
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2.0k
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Sex estimation problems in [estimateCellCounts]: methylation arrays
methylationArrayAnalysis minfiData minfi MethylationArrayData MethylationArray
updated 2.8 years ago by 68k • written 2.8 years ago by • 0
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5
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2.3k
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minfi error read.metharray.exp
methylationArrayAnalysis minfiData minfi MethylationArrayData MethylationArray
written 2.8 years ago by • 0
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1
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1.1k
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Job: 'Omics data analyst for HPCBio, University of Illinois
SingleCell rnaseq methylationArrayAnalysis Spatial
written 3.0 years ago by ★ 2.0k
0
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3
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4.6k
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Error: BiocParallel errors 1 remote errors, element index: 1 506 unevaluated and other errors first remote error:
methylationArrayAnalysis
updated 2.4 years ago by • 0 • written 3.1 years ago by • 0
0
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7
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3.9k
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ERROR happens when install "DSS" package
methylationArrayAnalysis ChAMP DMP DSS
updated 3.1 years ago by 68k • written 3.6 years ago by • 0
0
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1.1k
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filtering options in RnBeads for array data
Epigenetics RnBeads MethylationArrayData methylationArrayAnalysis
3.7 years ago Jitendra ▴ 10
0
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0
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1.4k
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getsex function error.
QualityControl methylationArrayAnalysis
3.9 years ago zusman • 0
2
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4
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2.0k
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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
3.9 years ago Jojo • 0
0
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6
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4.9k
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Merge problems in R
methylationArrayAnalysis ChAMP MethylationArrayData
4.4 years ago FWNL15 • 0
0
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2
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1.4k
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Limma experiment design and making contrasts
limma methylationArrayAnalysis
4.7 years ago Kesava • 0
1
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8
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2.2k
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EPIC array single replicate pipeline?
minfi methylationArrayAnalysis
4.7 years ago chay • 0
0
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2
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1.9k
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champ.SVD() : Error in while (step == 0) { : missing value where TRUE/FALSE needed
methylationArrayAnalysis EPICarray ChAMP Champ.SVD
4.7 years ago arisarkar88 ▴ 40
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2
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1.4k
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Error myDMP not found
Illumina methylationArrayAnalysis ChAMPdata ChAMP
4.9 years ago sissialva21 • 0
2
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7
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3.8k
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Blood cell composition adjustment in methylation EPIC array: ChAMP
MethylationArray methylationArrayAnalysis ChAMP
updated 2.2 years ago by • 0 • written 5.0 years ago by ▴ 20
1
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1
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1.7k
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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 5.1 years ago by 68k • written 5.1 years ago by • 0
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Answer: NUPOP usage by shepherl 4.2k
You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
Comment: How can I correctly use phyloseq with Docker? by fnfgame • 0
In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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