Showing : methylationArrayAnalysis • reset
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Unable to find sample sheet file for ChAMP methylation data analysis
MethylationArray MethylationArrayData methylationArrayAnalysis
updated 6 days ago by 67k • written 6 days ago by • 0
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13
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1.1k
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When doing differential methylation using the sesame package, seems to only go one way
methylation sesame methylationArrayAnalysis
updated 4 months ago by ▴ 20 • written 4 months ago by ▴ 10
1
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2
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585
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In the sesame package, what does the estimate output mean from testEnrichment()
MethylationArray methylation sesame methylationArrayAnalysis
4 months ago ramiro.barrantes ▴ 10
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1
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352
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Annotating DMRs
MethylationArray MethylationArrayData methylationArrayAnalysis
updated 4 months ago by 67k • written 4 months ago by ▴ 10
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1
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552
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ChAMP analysis Error: Meth Matrix and UnMeth Matrix seems not paried correctly AND incomplete final line
MethylationArray methylationArrayAnalysis ChAMP
updated 9 weeks ago by • 0 • written 6 months ago by • 0
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7
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1.5k
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Methylation Analysis experiment design using Limma
DNAMethylation limma methylationArrayAnalysis
9 months ago hortense96 • 0
1
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1
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1.2k
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Need Advice: Issue with ChAMP Analysis - Meth and UnMeth Matrix Pairing Error
MethylationArray methylationArrayAnalysis ChAMP
updated 11 months ago by 67k • written 11 months ago by • 0
1
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4
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1.1k
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EPIC or EPICv2 demo data of brain samples. FlowSorted.DLPFC.EPIC Availability?
DNAMethylation MethylationArray methylationArrayAnalysis illumina
11 months ago mikat • 0
2
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4
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1.3k
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Correct the batch effect in methylation analysis in R
BatchEffect limma methylationArrayAnalysis
updated 13 months ago by 52k • written 13 months ago by • 0
3
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6
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1.2k
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Methylation data analysis
MethylationArrayData methylationArrayAnalysis
14 months ago aldea85 • 0
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1
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1.1k
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EPIC v2 demo data from blood samples
MethylationArray methylationArrayAnalysis
updated 16 months ago by 67k • written 16 months ago by • 0
1
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3
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929
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Merging Methylation data (M-values) with phenotypic data
MethylationArrayData methylationArrayAnalysis
updated 17 months ago by 67k • written 17 months ago by • 0
0
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1
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3.6k
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Warning messages in detecting P-values
minfiDataEPIC methylationArrayAnalysis
updated 18 months ago by ★ 4.6k • written 18 months ago by ▴ 10
1
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2
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895
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edgeR, RRBS Library size preparation
RRBSdata edgeR methylationArrayAnalysis
19 months ago Krzysztof • 0
1
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2
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1.1k
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How to perform a methylation analyisis from m values
MethylationArrayData methylationArrayAnalysis
20 months ago • updated 19 months ago Irene • 0
1
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1
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812
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urgent error for producing table of topGO() annotated DMPs methylation
methylationArrayAnalysis topGO missMethyl MethylationArrayData MethylationArray
updated 21 months ago by ▴ 40 • written 21 months ago by • 0
2
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6
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1.5k
views
cpg.annotate() in DMRcate error
DNAMethylation methylationArrayAnalysis DMRcate MethylationArrayData MethylationArray
updated 21 months ago by ▴ 200 • written 21 months ago by • 0
0
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2
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1.5k
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Error in loading file using champ.load() from ChAMP package
champ.load epicarray ChAMP methylationArrayAnalysis
21 months ago arisarkar88 ▴ 40
0
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1
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779
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LmFit error in EPIC methylation array analysis, Minfi
methylationArrayAnalysis minfi MethylationArrayData minfiDataEPIC MethylationArray
updated 22 months ago by 52k • written 22 months ago by • 0
0
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1
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891
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specifying comparison of interest in the minfi Bumhunter function
limma bumphunter methylationArrayAnalysis minfi
updated 22 months ago by 67k • written 23 months ago by • 0
5
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1
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1.9k
views
Support for new Illumina human methylation EPIC array v2
human methylationArrayAnalysis
updated 12 months ago by • 0 • written 23 months ago by ▴ 80
0
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4
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1.5k
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Sex estimation problems in [estimateCellCounts]: methylation arrays
methylationArrayAnalysis minfiData minfi MethylationArrayData MethylationArray
updated 23 months ago by 67k • written 23 months ago by • 0
0
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5
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1.8k
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minfi error read.metharray.exp
methylationArrayAnalysis minfiData minfi MethylationArrayData MethylationArray
written 23 months ago by • 0
0
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1
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870
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Job: 'Omics data analyst for HPCBio, University of Illinois
SingleCell rnaseq methylationArrayAnalysis Spatial
written 2.1 years ago by ★ 2.0k
0
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3
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3.9k
views
Error: BiocParallel errors 1 remote errors, element index: 1 506 unevaluated and other errors first remote error:
methylationArrayAnalysis
updated 18 months ago by • 0 • written 2.3 years ago by • 0
0
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7
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3.3k
views
ERROR happens when install "DSS" package
methylationArrayAnalysis ChAMP DMP DSS
updated 2.3 years ago by 67k • written 2.7 years ago by • 0
0
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0
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935
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filtering options in RnBeads for array data
Epigenetics RnBeads MethylationArrayData methylationArrayAnalysis
2.8 years ago Jitendra ▴ 10
0
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0
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1.2k
views
getsex function error.
QualityControl methylationArrayAnalysis
3.0 years ago zusman • 0
2
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4
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1.6k
views
How to get methylation data in count data format from "Infinium MethylationEPIC BeadChips (Illumina)" idat files
methylationArrayAnalysis illuminaio beadarray DSS bsseqData
3.0 years ago Jojo • 0
0
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6
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4.0k
views
Merge problems in R
methylationArrayAnalysis ChAMP MethylationArrayData
3.5 years ago FWNL15 • 0
0
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2
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1.2k
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Limma experiment design and making contrasts
limma methylationArrayAnalysis
3.8 years ago Kesava • 0
1
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8
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1.8k
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EPIC array single replicate pipeline?
minfi methylationArrayAnalysis
3.8 years ago chay • 0
0
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2
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1.6k
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champ.SVD() : Error in while (step == 0) { : missing value where TRUE/FALSE needed
methylationArrayAnalysis EPICarray ChAMP Champ.SVD
3.8 years ago arisarkar88 ▴ 40
0
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2
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1.1k
views
Error myDMP not found
Illumina methylationArrayAnalysis ChAMPdata ChAMP
4.0 years ago sissialva21 • 0
2
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7
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3.1k
views
Blood cell composition adjustment in methylation EPIC array: ChAMP
MethylationArray methylationArrayAnalysis ChAMP
updated 15 months ago by • 0 • written 4.1 years ago by ▴ 20
1
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1
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1.4k
views
Error in read.metharray(basenames = files, extended = extended, verbose = verbose, : The following specified files do not exist:201172580052_R02C…
ArrayExpress methylationArrayAnalysis
updated 4.3 years ago by 67k • written 4.3 years ago by • 0
36 results • Page 1 of 1
Recent ...
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Answer: I am having issues with bowtie2_build by James W. MacDonald 67k
Is proof.fa an actual FASTA file? Have you tried using the demo data that comes with the package? See the [vignette under Build Bowtie Inde…
Answer: DEG analysis across multiple timepoints, treatments and tissues by Michael Love 43k
Yes, if you think the entire time course can be modified by tissue effects then you would include another set of interaction terms. I re…
Comment: How to visualize these pathways using pathview by Guido Hooiveld ★ 4.1k
FYI: a similar, if not identical issue has been reported before (`pathview` has problems visualizing some pathways, but not all). You likel…
Comment: Why select top highly expressed genes based on normalized counts, but then plot by Quang NN ▴ 10
I see. Thank you ATpoint!
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by Prakash Sah • 0
Thanks James!
Votes
Answer: Unable to install nloptr
Answer: ensembldb for Homo Sapiens organism containing superfluous SYMBOL genes?
C: How does edgeR cpm function calculate log(CPM) values?
Answer: Selection of correct coefficients or contrasts in DESeq2
Answer: Selection of correct coefficients or contrasts in DESeq2
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