Showing : MethylationArrayData • reset
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Mismatch between Illumina Mouse Methylation BeadChip annotation and genome browsers (UCSC/Ensembl)
methylationArrayAnalysis MethylationArrayData
updated 10 months ago by 68k • written 10 months ago by • 0
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719
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Conumee for EPIC and EPICv2 copy number
conumee CopyNumberVariation MethylationArrayData
11 months ago Adam • 0
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Methylation data - different probes are classified differently based on transcript? (Illumina methylation arrays, using minfi)
minf minfiDataEPIC MethylationArrayData MethylationArray EPICv2manifest
12 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
12 months ago a.alkema • 0
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445
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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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776
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Annotating DMRs
MethylationArray MethylationArrayData methylationArrayAnalysis
updated 17 months ago by 68k • written 17 months ago by ▴ 10
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657
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TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray normalize450K TCGAbiolinks Normalization MethylationArrayData
23 months ago Giovanni Calice ▴ 160
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Normalization in methylation analysis
Methylation minfi preprocessQuantile MethylationArrayData preprocessFunnorm
2.2 years ago kyj2226 • 0
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6
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1.7k
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Methylation data analysis
MethylationArrayData methylationArrayAnalysis
2.3 years ago • updated 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 2.5 years ago by 68k • written 2.5 years ago by • 0
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Read methylation data from tar files on GEO (GSE73303)
GeneExpression Bioconductor GEOquery MethylationArrayData
2.6 years ago Arianna • 0
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2
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1.7k
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How to perform a methylation analyisis from m values
MethylationArrayData methylationArrayAnalysis
2.7 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 2.8 years ago by ▴ 40 • written 2.8 years ago by • 0
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6
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2.1k
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cpg.annotate() in DMRcate error
DNAMethylation methylationArrayAnalysis DMRcate MethylationArrayData MethylationArray
updated 2.8 years ago by ▴ 230 • written 2.8 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 2.9 years ago by 53k • written 2.9 years ago by • 0
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4
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2.1k
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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
3.3 years ago shuangshuang • 0
2
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2
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2.2k
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Limma vs. lm for methylation data
limma MethylationArrayData MethylationArray
3.9 years ago • updated 3.8 years ago fluentin44 • 0
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1.2k
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filtering options in RnBeads for array data
Epigenetics RnBeads MethylationArrayData methylationArrayAnalysis
3.9 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
4.2 years ago Paulina • 0
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1.3k
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DNA methylation EPIC array and ChromHMM
chromhmmData MethylationArrayData
4.5 years ago macsue.jacques ▴ 10
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1.4k
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minfi - estimateCellCounts2-proportions sum more than 1
minfi minfiData MethylationArrayData
4.5 years ago ponche_de_kiwi • 0
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6
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5.0k
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Merge problems in R
methylationArrayAnalysis ChAMP MethylationArrayData
4.6 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 4.7 years ago by ▴ 780 • written 4.7 years ago by • 0
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0
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1.7k
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How to get illumina CpG IDs by gene name?
MethylationArrayData RnBeads
5.0 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
5.0 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 5.3 years ago by 68k • written 5.3 years ago by • 0
28 results • Page 1 of 1
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Comment: Which preprocessing steps are needed before running limpa? by miro165sabo • 0
Hi @gordonsmyth, thank you a lot for very fast and valuable response. I edited the question to provide more details.
Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ? by Gordon Smyth 53k
I tend to use dpcCN(), because it more robust than dpc() to experiments with lots of samples and big differences between samples. You coul…
Answer: Which preprocessing steps are needed before running limpa? by Gordon Smyth 53k
Please see the example limpa analyses given at <http://github.com/smythlab/limpa>, especially the kidney cancer case study. limpa does not…
Comment: Why does IDTaxa trainingSet for SILVA contain "_2" suffixes in the taxonomy name by Korneel • 0
Thanks for the quick reply! If I understand correctly, I think if I keep track of the full lineage, I shouldn't have any risk of collapsin…
Comment: Pathway abundance data from Curatedmetagenomics by yesquokkan • 0
Hello, I was also wondering about the same issue. Did you figure it out?
Votes
Answer: Which preprocessing steps are needed before running limpa?
Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ?
Answer: Which preprocessing steps are needed before running limpa?
Answer: Which preprocessing steps are needed before running limpa?
Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ?
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