Showing : methylationArrayAnalysis • reset
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Mismatch between Illumina Mouse Methylation BeadChip annotation and genome browsers (UCSC/Ensembl)
methylationArrayAnalysis MethylationArrayData
updated 7 weeks ago by 68k • written 7 weeks ago by • 0
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Correlation threshold
MethylationArray methylationArrayAnalysis StatisticalMethod
7 weeks ago user_bioinfo • 0
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2
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325
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Conumee2 - CNV.summaryplot()
conumee CopyNumberVariation MethylationAnalysis methylationArrayAnalysis EPICv2manifest
updated 11 weeks ago by 68k • written 11 weeks ago by • 0
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2
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Meffil: error in functional normalization function (Error in rg.to.mu(rg, probes))
methylationArrayAnalysis Normalization Epigenetics MethylationArrayData
3 months ago a.alkema • 0
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236
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Unable to find sample sheet file for ChAMP methylation data analysis
MethylationArray MethylationArrayData methylationArrayAnalysis
updated 3 months ago by 68k • written 3 months ago by • 0
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When doing differential methylation using the sesame package, seems to only go one way
methylation sesame methylationArrayAnalysis
updated 8 months ago by ▴ 20 • written 8 months ago by ▴ 10
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In the sesame package, what does the estimate output mean from testEnrichment()
MethylationArray methylation sesame methylationArrayAnalysis
8 months ago ramiro.barrantes ▴ 10
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522
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Annotating DMRs
MethylationArray MethylationArrayData methylationArrayAnalysis
updated 8 months ago by 68k • written 8 months ago by ▴ 10
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743
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ChAMP analysis Error: Meth Matrix and UnMeth Matrix seems not paried correctly AND incomplete final line
MethylationArray methylationArrayAnalysis ChAMP
updated 5 months ago by • 0 • written 10 months ago by • 0
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Methylation Analysis experiment design using Limma
DNAMethylation limma methylationArrayAnalysis
13 months ago hortense96 • 0
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1.5k
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Need Advice: Issue with ChAMP Analysis - Meth and UnMeth Matrix Pairing Error
MethylationArray methylationArrayAnalysis ChAMP
updated 15 months ago by 68k • written 15 months ago by • 0
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1.3k
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EPIC or EPICv2 demo data of brain samples. FlowSorted.DLPFC.EPIC Availability?
DNAMethylation MethylationArray methylationArrayAnalysis illumina
15 months ago mikat • 0
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1.5k
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Correct the batch effect in methylation analysis in R
BatchEffect limma methylationArrayAnalysis
updated 17 months ago by 52k • written 17 months ago by • 0
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6
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1.4k
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Methylation data analysis
MethylationArrayData methylationArrayAnalysis
18 months ago aldea85 • 0
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1.3k
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EPIC v2 demo data from blood samples
MethylationArray methylationArrayAnalysis
updated 19 months ago by 68k • written 19 months ago by • 0
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1.1k
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Merging Methylation data (M-values) with phenotypic data
MethylationArrayData methylationArrayAnalysis
updated 21 months ago by 68k • written 21 months ago by • 0
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3.8k
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Warning messages in detecting P-values
minfiDataEPIC methylationArrayAnalysis
updated 22 months ago by ★ 4.8k • written 22 months ago by ▴ 20
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978
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edgeR, RRBS Library size preparation
RRBSdata edgeR methylationArrayAnalysis
22 months ago Krzysztof • 0
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2
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1.2k
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How to perform a methylation analyisis from m values
MethylationArrayData methylationArrayAnalysis
23 months ago Irene • 0
1
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1
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907
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urgent error for producing table of topGO() annotated DMPs methylation
methylationArrayAnalysis topGO missMethyl MethylationArrayData MethylationArray
updated 2.1 years ago by ▴ 40 • written 2.1 years ago by • 0
2
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6
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1.7k
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cpg.annotate() in DMRcate error
DNAMethylation methylationArrayAnalysis DMRcate MethylationArrayData MethylationArray
updated 2.1 years ago by ▴ 230 • written 2.1 years ago by • 0
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1.6k
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Error in loading file using champ.load() from ChAMP package
champ.load epicarray ChAMP methylationArrayAnalysis
2.1 years ago • updated 2.0 years ago arisarkar88 ▴ 40
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919
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LmFit error in EPIC methylation array analysis, Minfi
methylationArrayAnalysis minfi MethylationArrayData minfiDataEPIC MethylationArray
updated 2.1 years ago by 52k • written 2.1 years ago by • 0
0
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967
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specifying comparison of interest in the minfi Bumhunter function
limma bumphunter methylationArrayAnalysis minfi
updated 2.2 years ago by 68k • written 2.2 years ago by • 0
5
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1
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2.1k
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Support for new Illumina human methylation EPIC array v2
human methylationArrayAnalysis
updated 16 months ago by • 0 • written 2.2 years ago by ▴ 80
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4
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1.7k
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Sex estimation problems in [estimateCellCounts]: methylation arrays
methylationArrayAnalysis minfiData minfi MethylationArrayData MethylationArray
updated 2.2 years ago by 68k • written 2.2 years ago by • 0
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5
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2.1k
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minfi error read.metharray.exp
methylationArrayAnalysis minfiData minfi MethylationArrayData MethylationArray
written 2.2 years ago by • 0
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1
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940
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Job: 'Omics data analyst for HPCBio, University of Illinois
SingleCell rnaseq methylationArrayAnalysis Spatial
written 2.4 years ago by ★ 2.0k
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3
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Error: BiocParallel errors 1 remote errors, element index: 1 506 unevaluated and other errors first remote error:
methylationArrayAnalysis
updated 22 months ago by • 0 • written 2.6 years ago by • 0
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7
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3.6k
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ERROR happens when install "DSS" package
methylationArrayAnalysis ChAMP DMP DSS
updated 2.6 years ago by 68k • written 3.0 years ago by • 0
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992
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filtering options in RnBeads for array data
Epigenetics RnBeads MethylationArrayData methylationArrayAnalysis
3.1 years ago Jitendra ▴ 10
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1.3k
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getsex function error.
QualityControl methylationArrayAnalysis
3.3 years ago zusman • 0
2
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4
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1.8k
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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
3.3 years ago Jojo • 0
0
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6
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4.5k
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Merge problems in R
methylationArrayAnalysis ChAMP MethylationArrayData
3.8 years ago FWNL15 • 0
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2
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1.2k
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Limma experiment design and making contrasts
limma methylationArrayAnalysis
4.1 years ago Kesava • 0
1
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8
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1.9k
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EPIC array single replicate pipeline?
minfi methylationArrayAnalysis
4.1 years ago chay • 0
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2
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1.7k
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champ.SVD() : Error in while (step == 0) { : missing value where TRUE/FALSE needed
methylationArrayAnalysis EPICarray ChAMP Champ.SVD
4.1 years ago arisarkar88 ▴ 40
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2
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1.2k
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Error myDMP not found
Illumina methylationArrayAnalysis ChAMPdata ChAMP
4.3 years ago sissialva21 • 0
2
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7
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3.5k
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Blood cell composition adjustment in methylation EPIC array: ChAMP
MethylationArray methylationArrayAnalysis ChAMP
updated 19 months ago by • 0 • written 4.4 years ago by ▴ 20
1
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1
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1.6k
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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 4.6 years ago by 68k • written 4.6 years ago by • 0
40 results • Page 1 of 1
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Answer: Typo in the help of lmFit() by Gordon Smyth 52k
Thanks for the heads-up. > The _Details_ in the documentation of lmFit() still says that the default correlation is 0.75 Yes, you're righ…
Comment: Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatm by caroline.zanchi ▴ 10
Thank you ! ![enter image description here][1] In the end I did ```r rn2 <- select(org.Dm.eg.db, row.names(cent_expr_matrix), "GENENAME"…
Answer: Memory issue while using "quickcluster" and "computeSumFactors" functions on sin by James W. MacDonald 68k
The obvious solution is to use cloud computing, which is likely cheaper than getting more RAM for your computer.
Answer: Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatm by James W. MacDonald 68k
``` library(org.Dm.eg.db) rn <- select(org.Dm.eg.db, row.names(cent_expr_matrix), "SYMBOL","FLYBASE") ## ensure no NA values get propaga…
Comment: Discrepancies in normalised count data vs unnormalised by AMgroup • 0
Thank you for your explanation, that makes sense. Do you have any suggestions on how to deal with this issue? if it is an issue? especially…
Votes
Answer: Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatm
Answer: Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatm
Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)
Comment: Check removeBatchEffect effectiveness
Answer: Check removeBatchEffect effectiveness
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