Showing : methylation • reset
14
votes
12
replies
9.2k
views
limma lmFit coefficients and p-values
limma methylation ewas
updated 7.7 years ago by ★ 13k • written 7.7 years ago by ▴ 30
6
votes
14
replies
4.7k
views
How to correctly import Bismark coverage files into bsseq?
bsseq bismark methylation
8.4 years ago enricoferrero ▴ 660
5
votes
9
replies
1.7k
views
limma Multi-level Experiments correcting for continuous covariates
limma epic methylation limma design matrix covariates
updated 5.6 years ago by ★ 28k • written 5.6 years ago by • 0
4
votes
4
replies
1.2k
views
Illumina Methylation 27k minfi
microarray methylation illumina27k minfi
updated 5.1 years ago by ★ 6.5k • written 5.1 years ago by • 0
4
votes
4
replies
3.0k
views
bumphunter output clarification: p values achieved with b=1000: further correction needed?
methylation dmr analysis bumphunter
updated 7.3 years ago by 65k • written 7.3 years ago by • 0
4
votes
8
replies
3.7k
views
minfi MethylationEPIC errors
minfi methylation IlluminaHumanMethylationEPICmanifest IlluminaHumanMethylationEPICanno.ilmn10b.hg19
updated 8.1 years ago by ★ 6.5k • written 8.1 years ago by ▴ 40
3
votes
1
reply
1.2k
views
Limma -decideTests interpretation for M-values
limma decidetests methylation
updated 8.1 years ago by 21k • written 8.1 years ago by ▴ 10
3
votes
5
replies
1.4k
views
DMRcate: Cpgids in DMR
methylation Epic annotation DMRcate
updated 4.5 years ago by 65k • written 4.5 years ago by ▴ 10
3
votes
15
replies
4.4k
views
Installing MethylationEPIC minifest and annotation
minfi methylation illuminahumanmethylationepicmanifest illumina
8.0 years ago rasii • 0
3
votes
1
reply
1.2k
views
two 450K methylation array manifests. where is the difference?
methylation 450k
8.2 years ago Pablo marin-garcia ▴ 90
3
votes
1
reply
1.5k
views
Limma Model Design
limma methylation microarray
updated 6.9 years ago by ★ 28k • written 6.9 years ago by • 0
2
votes
11
replies
9.1k
views
Minfi error in reading Basename column
methylation minfi
updated 7.5 years ago by ▴ 60 • written 8.6 years ago by • 0
2
votes
1
reply
969
views
lumi: Importing Methylation EPIC IDAT files
lumi EPIC Methylation
4.0 years ago Zach Roe ▴ 10
2
votes
16
replies
2.5k
views
Methylation EPIC array: ChAMP package-champ.load added probes?
methylation epic champ champ.load() Methylation array
updated 4.3 years ago by ▴ 270 • written 4.3 years ago by ▴ 20
2
votes
3
replies
2.1k
views
"Seems your IDAT file not from one Array"
EPIC methylation ChAMP
updated 6.0 years ago by ▴ 30 • written 6.0 years ago by • 0
2
votes
8
replies
1.9k
views
edgeR: design matrix for methylation analysis
edger methylation
updated 5.6 years ago by 50k • written 5.8 years ago by • 0
2
votes
0
replies
1.2k
views
Job: Two Post-doctoral positions at the CRUK Cambridge Institute
cancer methylation rna-seq Job
7.9 years ago Andy Lynch ▴ 120
2
votes
1
reply
1.3k
views
EPIC methylation array - analysis with ChAMP - how to export bed/wig file to view in UCSC/IGV?
methylation epic champ
updated 5.4 years ago by ▴ 270 • written 5.4 years ago by ▴ 10
2
votes
1
reply
642
views
Limma model orientation
limma methylation MethylationArray
updated 23 months ago by 65k • written 23 months ago by • 0
2
votes
2
replies
1.4k
views
dmrseq: cannot adjust for a covariate
dmrseq dmr dmrs bisulfite methylation
updated 6.2 years ago by ▴ 60 • written 6.2 years ago by • 0
2
votes
2
replies
850
views
How to overcome issue linked to loading big R object
minfi R methylation
3.0 years ago Federica ▴ 10
2
votes
2
replies
1.3k
views
Package for iScan methylation data
methylation iscan
9.5 years ago Brian Smith ▴ 120
2
votes
2
replies
2.5k
views
Illumina 450k Annotation Definitions/Articles: How was "Enhancer" status determined?
probe annotation illimina 450k methylation minfi methylation
8.8 years ago metamaden ▴ 10
1
vote
3
replies
1.3k
views
Skewed beta-distribution from Methylation EPIC array data
ChAMP EPIC Illumina Methylation
4.2 years ago erwin.tomasich ▴ 10
1
vote
2
replies
1.4k
views
Problem installing ChAMP package.
software error microarray champ methylation
updated 5.7 years ago by 25k • written 5.7 years ago by ▴ 10
1
vote
1
reply
932
views
SVA paired samples
SVA EPIC methylation limma
updated 4.1 years ago by 65k • written 4.1 years ago by • 0
1
vote
3
replies
1.0k
views
trackViewer: how to make lolliplots for methylation data
trackViewer methylation lolliplot
4.5 years ago patriciasolesanchez • 0
1
vote
9
replies
2.6k
views
bumphunter beta values
methylation minfi bumphunter
updated 8.0 years ago by 65k • written 8.0 years ago by ▴ 40
1
vote
4
replies
1.4k
views
M3D package in Bioconductor 3.4
bioconductor methylation
updated 7.4 years ago by ▴ 80 • written 7.4 years ago by • 0
1
vote
1
reply
807
views
Issue with ChAMP DMP.GUI
ChAMP champ methylation EPIC
updated 4.2 years ago by ▴ 90 • written 4.3 years ago by • 0
1
vote
5
replies
2.8k
views
About methylation data processing
methylation
updated 8.2 years ago by ▴ 740 • written 8.2 years ago by ▴ 290
1
vote
3
replies
1.4k
views
Combining pfilter (wateRmelon) and preprocessNoob (minfi)
wateRmelon minfi methylation pfilter preprocessNoob
updated 4.6 years ago by ▴ 10 • written 4.6 years ago by • 0
1
vote
3
replies
1.0k
views
Differential methylation probes were much fewer than differential methylation genes
methylation limma
updated 4.4 years ago by 65k • written 4.4 years ago by • 0
1
vote
2
replies
1.4k
views
Methylation data visualization using methyAnalysis with minfi
methylation microarray illumina minfi methyanalysis
updated 5.3 years ago by ★ 1.3k • written 5.4 years ago by • 0
1
vote
2
replies
2.0k
views
Minfi read.metharray.sheet error
minfi methylation dataimport minfidata missmethyl
updated 5.6 years ago by 65k • written 5.6 years ago by ▴ 20
1
vote
2
replies
3.6k
views
minfi error in read.metharray
minfi methylation idat samplesheet
updated 3.0 years ago by • 0 • written 5.0 years ago by • 0
1
vote
1
reply
1.9k
views
Extracting gene structures from a GFF3 file for use with annotateWithGeneParts()
genomicfeatures genomation genomicranges methylation annotation
updated 5.7 years ago by ▴ 20 • written 5.7 years ago by • 0
1
vote
0
replies
1.6k
views
Multiple linear regression model for DMR detection?
methylation linear model dmr bsseq biseq
8.4 years ago enricoferrero ▴ 660
1
vote
1
reply
1.7k
views
How to convert Illumina HumanMethylation27 BeadChip ID's to gene names?
gene names methylation illumina convertids
updated 5.9 years ago by 65k • written 5.9 years ago by ▴ 10
1
vote
4
replies
1.5k
views
dmrseq error: promise already under evaluation??
dmrseq Methylation
updated 4.8 years ago by ▴ 60 • written 4.8 years ago by • 0
1
vote
2
replies
1.5k
views
minfi package QC report error?
minfi methylation illumina
9.5 years ago Brian Smith ▴ 120
1
vote
1
reply
1.2k
views
Not getting Adjusted p-values from multtest package
multtest methylation adjusted pvalue
updated 8.4 years ago by ▴ 110 • written 8.4 years ago by ▴ 10
1
vote
5
replies
1.3k
views
Understanding methyAnalysis Results
methyAnalysis methyanalysis methylation illuminahumanmethylation450k.db
updated 9.1 years ago by ▴ 80 • written 9.1 years ago by ▴ 370
1
vote
5
replies
4.1k
views
minfi - error when reading idat files
minfi methylation
updated 19 months ago by • 0 • written 6.8 years ago by ▴ 10
1
vote
8
replies
3.3k
views
Normalization starting from beta values in minfi
methylation minfi
written 7.9 years ago by ▴ 290
1
vote
2
replies
2.5k
views
BS-seq differential methylation analysis using continuous variable
dmr methylation deseq2 bsseq biseq
updated 8.5 years ago by ★ 6.5k • written 8.5 years ago by ▴ 660
1
vote
3
replies
1.5k
views
coef in dmrcate
dmrcate bumphunter methylation epic
updated 7.0 years ago by 65k • written 7.0 years ago by ▴ 10
1
vote
9
replies
3.6k
views
strange results from differential methylation analysis using limma
limma methylation methyanalysis IMA
updated 23 months ago by 21k • written 7.1 years ago by • 0
1
vote
2
replies
1.5k
views
DMRcate results file ordered by genomic location and not Stouffer p-val?
DMRcate dmrcate methylation
updated 6.9 years ago by ▴ 170 • written 6.9 years ago by • 0
1
vote
3
replies
1.4k
views
Minfi returning incorrect beta values
minfi illumina illumina450k methylation R
6.8 years ago ezrabekele17 • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Estimating Cell Counts for EPIC V2 array data by normawiedman059 • 0
0 [103] spam_2.9-1 doParallel_1.0.17 iterators_1.0.14 [106] foreach_1.5.2 beeswarm_0.4.0 tgp_2.4-20 [109] beanplot_1.3.1 fpc_2.2-9 dbscan_1…
Comment: Finding DEGs by using edgeR by Gordon Smyth 50k
Filtering (removing lowly expressed genes) is separate to normalization. It isn't clear why not subsetting would cause any difficulty. It …
Comment: How to make DGEList and design matrix by edgeR package by prity6459 • 0
Thank you for your suggestion. Yes, I have made DGEList and design matrix in my script. But I was not entirely confident while making thos…
Comment: Finding DEGs by using edgeR by prity6459 • 0
Hello Gordon, Thanks for your response. By normalization, I meant that I have already removed lowly expressed genes from my count matrix. …
Answer: FilterByExpr low counts with small sample size by Gordon Smyth 50k
It doesn't seem to me that there is necessarily any problem with the analysis. You say that there are "too many low-reads" but actually th…
Votes
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Comment: DEXSeq DEXSeqDataSet count matrix duplication
Awards • All
Popular Question to BioinfGuru ▴ 20
Popular Question to Gordon Smyth 50k
Scholar to Peter Hickey ▴ 740
Popular Question to sropri • 0
Popular Question to W. Evan Johnson ▴ 850
Locations • All
Switzerland, just now
University of Applied Sciences Upper Austria, Hagenberg, Austria, 2 minutes ago
WEHI, Melbourne, Australia, 4 minutes ago
France, 8 minutes ago
Ireland, 24 minutes ago
Traffic: 863 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