Showing : MethylationArrayData • reset
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Mismatch between Illumina Mouse Methylation BeadChip annotation and genome browsers (UCSC/Ensembl)
methylationArrayAnalysis MethylationArrayData
updated 9 months ago by 68k • written 9 months ago by • 0
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631
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Conumee for EPIC and EPICv2 copy number
conumee CopyNumberVariation MethylationArrayData
10 months ago Adam • 0
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376
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Methylation data - different probes are classified differently based on transcript? (Illumina methylation arrays, using minfi)
minf minfiDataEPIC MethylationArrayData MethylationArray EPICv2manifest
11 months ago charlie.wright • 0
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Meffil: error in functional normalization function (Error in rg.to.mu(rg, probes))
methylationArrayAnalysis Normalization Epigenetics MethylationArrayData
11 months ago a.alkema • 0
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414
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Unable to find sample sheet file for ChAMP methylation data analysis
MethylationArray MethylationArrayData methylationArrayAnalysis
updated 12 months ago by 68k • written 12 months ago by • 0
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741
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Annotating DMRs
MethylationArray MethylationArrayData methylationArrayAnalysis
updated 16 months ago by 68k • written 16 months ago by ▴ 10
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643
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TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray normalize450K TCGAbiolinks Normalization MethylationArrayData
22 months ago Giovanni Calice ▴ 160
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Normalization in methylation analysis
Methylation minfi preprocessQuantile MethylationArrayData preprocessFunnorm
2.1 years ago kyj2226 • 0
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1.7k
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Methylation data analysis
MethylationArrayData methylationArrayAnalysis
2.2 years ago aldea85 • 0
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3
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1.4k
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Merging Methylation data (M-values) with phenotypic data
MethylationArrayData methylationArrayAnalysis
updated 2.4 years ago by 68k • written 2.4 years ago by • 0
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Read methylation data from tar files on GEO (GSE73303)
GeneExpression Bioconductor GEOquery MethylationArrayData
2.5 years ago Arianna • 0
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2
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1.5k
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How to perform a methylation analyisis from m values
MethylationArrayData methylationArrayAnalysis
2.6 years ago Irene • 0
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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 2.7 years ago by ▴ 40 • written 2.7 years ago by • 0
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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 2.7 years ago by ▴ 230 • written 2.7 years ago by • 0
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1.1k
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LmFit error in EPIC methylation array analysis, Minfi
methylationArrayAnalysis minfi MethylationArrayData minfiDataEPIC MethylationArray
updated 2.8 years ago by 53k • written 2.8 years ago by • 0
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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 2.9 years ago by 68k • written 2.9 years ago by • 0
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5
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2.4k
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minfi error read.metharray.exp
methylationArrayAnalysis minfiData minfi MethylationArrayData MethylationArray
written 2.9 years ago by • 0
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2
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2.6k
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ChAMP package:Error in cmdscale(d) : 'k' must be in {1, 2, .. n - 1}
MethylationArrayData
3.2 years ago shuangshuang • 0
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2
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2.1k
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Limma vs. lm for methylation data
limma MethylationArrayData MethylationArray
3.8 years ago fluentin44 • 0
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1.1k
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filtering options in RnBeads for array data
Epigenetics RnBeads MethylationArrayData methylationArrayAnalysis
3.8 years ago Jitendra ▴ 10
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1.3k
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Problem loading Red channel idat files with champ.load
R MethylationArrayData ChAMP
4.1 years ago Paulina • 0
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1.3k
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DNA methylation EPIC array and ChromHMM
chromhmmData MethylationArrayData
4.4 years ago macsue.jacques ▴ 10
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1.3k
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minfi - estimateCellCounts2-proportions sum more than 1
minfi minfiData MethylationArrayData
4.4 years ago ponche_de_kiwi • 0
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6
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4.9k
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Merge problems in R
methylationArrayAnalysis ChAMP MethylationArrayData
4.5 years ago FWNL15 • 0
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1
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1.4k
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Error in reading metharray sheet
DifferentialMethylation MethylationArrayData
updated 4.6 years ago by ▴ 780 • written 4.6 years ago by • 0
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1.6k
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How to get illumina CpG IDs by gene name?
MethylationArrayData RnBeads
4.9 years ago D ▴ 10
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4
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3.9k
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Unable to read in the IDAT files using read.metharray.exp()
MethylationArrayData methy Bioconductor minfi
4.9 years ago shweta • 0
1
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1
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3.4k
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DMR Plot
dmr MethylationArrayData DMRcatedata
updated 5.2 years ago by 68k • written 5.2 years ago by • 0
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Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by ATpoint ★ 5.0k
Yes, still it's not reproducible, yet hard to debug. I cannot reproduce myself either.
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Benjamin • 0
Still happening using pre-existing size factors estimating dispersions gene-wise dispersion estimates: 15 workers mean-dis…
Answer: BiocParallel (and DESeq2) - wrong args for environment subassignment by Benjamin • 0
Still happening in a clean install
Comment: limpa analysis advice by Gordon Smyth 53k
Yes, we use Astral currently. The main dataset in the limpa preprint is Astral. I don't see any major problems with your data and I think …
Comment: limpa analysis advice by SamGG ▴ 360
Thank you for your comments. Please note that I did not apply any filtering to the peptide intensity. The experimental protocol includes tw…
Votes
Comment: limpa analysis advice
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
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