Showing : MethylationArray • reset
0
votes
0
replies
229
views
Correlation threshold
MethylationArray methylationArrayAnalysis StatisticalMethod
8 months ago user_bioinfo • 0
0
votes
0
replies
349
views
Methylation data - different probes are classified differently based on transcript? (Illumina methylation arrays, using minfi)
minf minfiDataEPIC MethylationArrayData MethylationArray EPICv2manifest
9 months ago charlie.wright • 0
0
votes
1
reply
372
views
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
1
vote
2
replies
556
views
Epic v2 Annotation CpG_maf source?
MethylationArray methy EPICv2manifest
12 months ago Meghan • 0
2
votes
1
reply
739
views
Question: How to Set Up Contrasts for Case-Control Analysis in Limma While Adjusting for Covariates?
MethylationArray EpigeneticsWorkflow limma Regression
updated 14 months ago by 68k • written 14 months ago by ▴ 20
1
vote
2
replies
1.1k
views
In the sesame package, what does the estimate output mean from testEnrichment()
MethylationArray methylation sesame methylationArrayAnalysis
14 months ago ramiro.barrantes ▴ 10
0
votes
1
reply
699
views
Annotating DMRs
MethylationArray MethylationArrayData methylationArrayAnalysis
updated 14 months ago by 68k • written 14 months ago by ▴ 10
1
vote
1
reply
806
views
Empty Results from champ.DMP Despite Expected Output
MethylationArray ChAMP R
updated 15 months ago by 68k • written 15 months ago by • 0
0
votes
3
replies
893
views
Open Sesame: in what genes are my differentially methylated probes!!
MethylationArray sesameData sesame
updated 12 months ago by • 0 • written 15 months ago by ▴ 10
0
votes
2
replies
1.8k
views
save.rnb.set warnings when trying to save rnb.set
RnBeads RnBeads.hg19 MethylationArray
updated 5 months ago by • 0 • written 16 months ago by • 0
0
votes
1
reply
927
views
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 16 months ago by • 0
0
votes
2
replies
2.1k
views
Batch effect correction: methylome data
sesame BatchEffect MethylationArray
updated 18 months ago by ▴ 20 • written 18 months ago by • 0
3
votes
2
replies
1.1k
views
limma Intercept vs No-intercept models completely changing DMR results?
limma DMRcate MethylationArray EPICV2
updated 18 months ago by 53k • written 19 months ago by • 0
1
vote
2
replies
2.5k
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation SequenceAnnotation MethylationArray GenomicDistributionsData
19 months ago Yveto • 0
0
votes
0
replies
615
views
TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray normalize450K TCGAbiolinks Normalization MethylationArrayData
21 months ago • updated 20 months ago Giovanni Calice ▴ 160
1
vote
3
replies
2.2k
views
Error in GOmeth function of missMethyl when EPICv2 annotation is used
DNAMethylation GO MethylationArray missMethyl EPICv2
21 months ago • updated 14 months ago s.malik • 0
0
votes
11
replies
1.9k
views
Strange logFC values in differential methylation site anslysis
edgeR MethylationArray
updated 21 months ago by 53k • written 21 months ago by • 0
1
vote
7
replies
1.8k
views
Library size normalization in methylation count analysis
edgeR MethylationArray
updated 13 months ago by • 0 • written 21 months ago by • 0
1
vote
1
reply
1.7k
views
Need Advice: Issue with ChAMP Analysis - Meth and UnMeth Matrix Pairing Error
MethylationArray methylationArrayAnalysis ChAMP
updated 21 months ago by 68k • written 21 months ago by • 0
0
votes
7
replies
1.4k
views
error in reading idat files and creating rgset
minfi MethylationArray
updated 21 months ago by 68k • written 21 months ago by • 0
1
vote
2
replies
1.1k
views
How to get normalized values for methylation counts in edgeR
edgeR MethylationArray
22 months ago • updated 21 months ago mico • 0
1
vote
4
replies
1.6k
views
EPIC or EPICv2 demo data of brain samples. FlowSorted.DLPFC.EPIC Availability?
DNAMethylation MethylationArray methylationArrayAnalysis illumina
22 months ago mikat • 0
0
votes
1
reply
1.4k
views
EPIC v2 demo data from blood samples
MethylationArray methylationArrayAnalysis
updated 2.1 years ago by 68k • written 2.1 years ago by • 0
5
votes
5
replies
1.6k
views
limma output for epic array methylation data
linearregression epicarray MethylationArray limma
2.3 years ago Jitendra ▴ 10
1
vote
1
reply
1.0k
views
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
votes
6
replies
1.9k
views
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
votes
1
reply
1.1k
views
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
votes
4
replies
2.0k
views
Sex estimation problems in [estimateCellCounts]: methylation arrays
methylationArrayAnalysis minfiData minfi MethylationArrayData MethylationArray
updated 2.7 years ago by 68k • written 2.7 years ago by • 0
0
votes
5
replies
2.3k
views
minfi error read.metharray.exp
methylationArrayAnalysis minfiData minfi MethylationArrayData MethylationArray
written 2.7 years ago by • 0
2
votes
1
reply
1.1k
views
Limma model orientation
limma methylation MethylationArray
updated 3.6 years ago by 68k • written 3.6 years ago by • 0
2
votes
2
replies
1.9k
views
Limma vs. lm for methylation data
limma MethylationArrayData MethylationArray
3.6 years ago fluentin44 • 0
0
votes
0
replies
1.4k
views
Surrogate variable, celltype composition correction and overfitting in DNA methylation data
sva limma methylation MethylationArray
4.9 years ago epibio ▴ 10
6
votes
6
replies
2.4k
views
Limma Paired Analysis - Force intercept to 0
MethylationArray limma
4.9 years ago • updated 4.8 years ago MoltenLight ▴ 10
2
votes
7
replies
3.8k
views
Blood cell composition adjustment in methylation EPIC array: ChAMP
MethylationArray methylationArrayAnalysis ChAMP
updated 2.1 years ago by • 0 • written 5.0 years ago by ▴ 20
0
votes
0
replies
931
views
Diffrential Gene expression in a group of specific methylated prometor patience
GeneExpression methyAnalysis MethylationArray
5.0 years ago coobzie • 0
35 results • Page 1 of 1
Recent ...
Replies
Comment: Generalized edgeR functions by Omar • 0
[ragdoll hit](https://ragdollhitstickman.io/) That actually sounds like a reasonable approach, especially if the overlapping intervals repr…
Comment: upstream git branches of bioc-release by TrentonCollier99 • 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments. https://bioc-release.r-univ…
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Ahmed Salah • 0
Thank you very much! will take that into consideration
Comment: Large logFC but somewhat high FDR by JKim • 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments.
Comment: upstream git branches of bioc-release by Jeroen ▴ 10
OK I have updated https://bioc-release.r-universe.dev accordingly. Let me know if you find version differences when mirroring binaries.
Votes
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
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
Awards • All
Popular Question to Gordon Smyth 53k
Popular Question to shepherl 4.2k
Popular Question to story.benjamin ▴ 20
Supporter to fabio.marroni • 0
Popular Question to Guido Hooiveld ★ 4.1k
Locations • All
United States, 17 minutes ago
United States, 21 minutes ago
United States, 1 hour ago
WEHI, Melbourne, Australia, 2 hours ago
India, 2 hours ago
Traffic: 811 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6