Showing : methylation • reset
14
votes
12
replies
5.0k
views
limma lmFit coefficients and p-values
limma methylation ewas
updated 4.9 years ago by 13k • written 4.9 years ago by ▴ 30
6
votes
14
replies
2.6k
views
How to correctly import Bismark coverage files into bsseq?
bsseq bismark methylation
5.5 years ago enricoferrero ▴ 570
5
votes
9
replies
604
views
limma Multi-level Experiments correcting for continuous covariates
limma epic methylation limma design matrix covariates
updated 2.8 years ago by ★ 26k • written 2.8 years ago by • 0
4
votes
8
replies
2.7k
views
minfi MethylationEPIC errors
minfi methylation IlluminaHumanMethylationEPICmanifest IlluminaHumanMethylationEPICanno.ilmn10b.hg19
updated 5.2 years ago by 6.5k • written 5.2 years ago by ▴ 40
4
votes
4
replies
1.6k
views
bumphunter output clarification: p values achieved with b=1000: further correction needed?
methylation dmr analysis bumphunter
updated 4.4 years ago by 57k • written 4.4 years ago by • 0
4
votes
4
replies
373
views
Illumina Methylation 27k minfi
microarray methylation illumina27k minfi
updated 2.3 years ago by 6.5k • written 2.3 years ago by • 0
3
votes
15
replies
2.7k
views
Installing MethylationEPIC minifest and annotation
minfi methylation illuminahumanmethylationepicmanifest illumina
5.2 years ago rasii • 0
3
votes
5
replies
246
views
DMRcate: Cpgids in DMR
methylation Epic annotation DMRcate
updated 20 months ago by 57k • written 20 months ago by ▴ 10
3
votes
1
reply
762
views
two 450K methylation array manifests. where is the difference?
methylation 450k
5.4 years ago Pablo marin-garcia ▴ 90
3
votes
1
reply
808
views
Limma -decideTests interpretation for M-values
limma decidetests methylation
updated 5.3 years ago by 21k • written 5.3 years ago by ▴ 10
3
votes
1
reply
1.1k
views
Limma Model Design
limma methylation microarray
updated 4.0 years ago by ★ 26k • written 4.0 years ago by • 0
2
votes
11
replies
6.0k
views
Minfi error in reading Basename column
methylation minfi
updated 4.7 years ago by ▴ 60 • written 5.8 years ago by • 0
2
votes
1
reply
145
views
lumi: Importing Methylation EPIC IDAT files
lumi EPIC Methylation
13 months ago Zach Roe ▴ 10
2
votes
16
replies
541
views
Methylation EPIC array: ChAMP package-champ.load added probes?
methylation epic champ champ.load() Methylation array
updated 17 months ago by ▴ 240 • written 17 months ago by • 0
2
votes
8
replies
622
views
edgeR: design matrix for methylation analysis
edger methylation
updated 2.7 years ago by 43k • written 3.0 years ago by • 0
2
votes
0
replies
645
views
Job: Two Post-doctoral positions at the CRUK Cambridge Institute
cancer methylation rna-seq Job
5.0 years ago Andy Lynch ▴ 100
2
votes
1
reply
464
views
EPIC methylation array - analysis with ChAMP - how to export bed/wig file to view in UCSC/IGV?
methylation epic champ
updated 2.6 years ago by ▴ 240 • written 2.6 years ago by • 0
2
votes
2
replies
102
views
How to overcome issue linked to loading big R object
minfi R methylation
6 weeks ago Federica ▴ 10
2
votes
2
replies
659
views
dmrseq: cannot adjust for a covariate
dmrseq dmr dmrs bisulfite methylation
updated 3.3 years ago by ▴ 60 • written 3.4 years ago by • 0
2
votes
3
replies
725
views
"Seems your IDAT file not from one Array"
EPIC methylation ChAMP
updated 3.2 years ago by ▴ 20 • written 3.2 years ago by • 0
2
votes
2
replies
731
views
Package for iScan methylation data
methylation iscan
6.7 years ago Brian Smith ▴ 120
2
votes
2
replies
1.6k
views
Illumina 450k Annotation Definitions/Articles: How was "Enhancer" status determined?
probe annotation illimina 450k methylation minfi methylation
5.9 years ago maden.sean ▴ 10
1
vote
1
reply
120
views
SVA paired samples
SVA EPIC methylation limma
updated 15 months ago by 57k • written 15 months ago by • 0
1
vote
9
replies
1.6k
views
bumphunter beta values
methylation minfi bumphunter
updated 5.2 years ago by 57k • written 5.2 years ago by ▴ 40
1
vote
2
replies
540
views
Problem installing ChAMP package.
software error microarray champ methylation
updated 2.8 years ago by 25k • written 2.8 years ago by ▴ 10
1
vote
3
replies
224
views
Differential methylation probes were much fewer than differential methylation genes
methylation limma
updated 19 months ago by 57k • written 19 months ago by • 0
1
vote
4
replies
734
views
M3D package in Bioconductor 3.4
bioconductor methylation
updated 4.5 years ago by ▴ 70 • written 4.5 years ago by • 0
1
vote
5
replies
1.7k
views
About methylation data processing
methylation
updated 5.3 years ago by ▴ 470 • written 5.3 years ago by ▴ 290
1
vote
1
reply
131
views
Issue with ChAMP DMP.GUI
ChAMP champ methylation EPIC
updated 17 months ago by ▴ 90 • written 17 months ago by • 0
1
vote
3
replies
192
views
Skewed beta-distribution from Methylation EPIC array data
ChAMP EPIC Illumina Methylation
16 months ago erwin.tomasich ▴ 10
1
vote
3
replies
194
views
trackViewer: how to make lolliplots for methylation data
trackViewer methylation lolliplot
19 months ago patriciasolesanchez • 0
1
vote
1
reply
69
views
Error in the UcscTrack() in package "Gviz"
DMR Methylation R Gviz
updated 5 weeks ago by ▴ 670 • written 5 weeks ago by • 0
1
vote
2
replies
821
views
minfi error in read.metharray
minfi methylation idat samplesheet
updated 8 weeks ago by • 0 • written 2.1 years ago by • 0
1
vote
2
replies
511
views
Methylation data visualization using methyAnalysis with minfi
methylation microarray illumina minfi methyanalysis
updated 2.5 years ago by ★ 1.2k • written 2.5 years ago by • 0
1
vote
4
replies
418
views
dmrseq error: promise already under evaluation??
dmrseq Methylation
updated 24 months ago by ▴ 60 • written 2.0 years ago by • 0
1
vote
2
replies
1.1k
views
minfi package QC report error?
minfi methylation illumina
6.7 years ago Brian Smith ▴ 120
1
vote
1
reply
701
views
How to convert Illumina HumanMethylation27 BeadChip ID's to gene names?
gene names methylation illumina convertids
updated 3.1 years ago by 57k • written 3.1 years ago by ▴ 10
1
vote
0
replies
1.1k
views
Multiple linear regression model for DMR detection?
methylation linear model dmr bsseq biseq
5.5 years ago enricoferrero ▴ 570
1
vote
2
replies
758
views
Minfi read.metharray.sheet error
minfi methylation dataimport minfidata missmethyl
updated 2.7 years ago by 57k • written 2.7 years ago by ▴ 20
1
vote
6
replies
281
views
Use intercept or not in model matrix for edgeR methylation analysis
edgeR R methylation GLM
22 months ago • updated 21 months ago sabrina.mcnew • 0
1
vote
1
reply
732
views
Not getting Adjusted p-values from multtest package
multtest methylation adjusted pvalue
updated 5.6 years ago by ▴ 110 • written 5.6 years ago by ▴ 10
1
vote
1
reply
476
views
Extracting gene structures from a GFF3 file for use with annotateWithGeneParts()
genomicfeatures genomation genomicranges methylation annotation
updated 2.9 years ago by ▴ 20 • written 2.9 years ago by • 0
1
vote
5
replies
789
views
Understanding methyAnalysis Results
methyAnalysis methyanalysis methylation illuminahumanmethylation450k.db
updated 6.3 years ago by ▴ 80 • written 6.3 years ago by ▴ 340
1
vote
3
replies
714
views
Minfi returning incorrect beta values
minfi illumina illumina450k methylation R
3.9 years ago ezrabekele17 • 0
1
vote
7
replies
1.8k
views
Normalization starting from beta values in minfi
methylation minfi
updated 5.0 years ago by 57k • written 5.0 years ago by ▴ 290
1
vote
2
replies
1.5k
views
BS-seq differential methylation analysis using continuous variable
dmr methylation deseq2 bsseq biseq
updated 5.7 years ago by 6.5k • written 5.7 years ago by ▴ 570
1
vote
3
replies
786
views
coef in dmrcate
dmrcate bumphunter methylation epic
updated 4.2 years ago by 57k • written 4.2 years ago by ▴ 10
1
vote
7
replies
1.8k
views
strange results from differential methylation analysis using limma
limma methylation methyanalysis IMA
updated 4.2 years ago by 43k • written 4.3 years ago by • 0
1
vote
2
replies
753
views
DMRcate results file ordered by genomic location and not Stouffer p-val?
DMRcate dmrcate methylation
updated 4.0 years ago by ▴ 120 • written 4.1 years ago by • 0
1
vote
3
replies
268
views
Combining pfilter (wateRmelon) and preprocessNoob (minfi)
wateRmelon minfi methylation pfilter preprocessNoob
updated 21 months ago by ▴ 10 • written 21 months ago by • 0
50 results • Page 1 of 1
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Answer: DESeq2: NA's in mcols(object)$betaConv by Michael Love 33k
Re: Q1, do these have all zero counts? If you run `vst(dds, blind=FALSE)` on a `dds` in which `DESeq()` has already been run, it will be…
Comment: DESeq2 - one groups with no replicates by SUMIT • 0
I disturb you only because I thought why I am not getting an error like deprecated in v1.20 and no longer supported...... Anyway, Thank you…
Answer: How to convert .CEL file to .VCF file? by James W. MacDonald 57k
I don't know of anything within Bioconductor, but after a Google search for affy2vcf (hint), I came upon [this github repo][1]. [1]:…
Answer: DESeq2: One or more designs for contrasts of interest by Michael Love 33k
Sorry, I can only provide software support at this time. I don’t have time to provide statistical consultation on the support site. I’d rec…
Answer: DESeq2 - one groups with no replicates by Michael Love 33k
You can perform this analysis, it should run in DESeq2, but I believe there are also some specialized methods to give a single sample somet…
Votes
Answer: scater::calculatePCA error when using BPPARAM = MulticoreParam
Answer: scater::calculatePCA error when using BPPARAM = MulticoreParam
Answer: DESeq2 - one groups with no replicates
Answer: DESeq2 - one groups with no replicates
pairwise combining factors or multifactor analysis ? (DESeq2)
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