Showing : Methylation • reset
14
votes
12
replies
9.3k
views
limma lmFit coefficients and p-values
limma methylation ewas
updated 7.8 years ago by ★ 13k • written 7.8 years ago by ▴ 30
6
votes
14
replies
4.8k
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 5.7 years ago by ★ 28k • written 5.7 years ago by • 0
4
votes
4
replies
1.3k
views
Illumina Methylation 27k minfi
microarray methylation illumina27k minfi
updated 5.2 years ago by ★ 6.5k • written 5.2 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
1.3k
views
Limma -decideTests interpretation for M-values
limma decidetests methylation
updated 8.2 years ago by 21k • written 8.2 years ago by ▴ 10
3
votes
5
replies
1.4k
views
DMRcate: Cpgids in DMR
methylation Epic annotation DMRcate
updated 4.6 years ago by 65k • written 4.6 years ago by ▴ 10
3
votes
15
replies
4.4k
views
Installing MethylationEPIC minifest and annotation
minfi methylation illuminahumanmethylationepicmanifest illumina
8.1 years ago rasii • 0
3
votes
1
reply
1.2k
views
two 450K methylation array manifests. where is the difference?
methylation 450k
8.3 years ago • updated 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
9.2k
views
Minfi error in reading Basename column
methylation minfi
updated 7.6 years ago by ▴ 60 • written 8.7 years ago by • 0
2
votes
1
reply
991
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 ▴ 280 • 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 6.1 years ago by ▴ 30 • written 6.1 years ago by • 0
2
votes
8
replies
2.0k
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 ▴ 280 • written 5.5 years ago by ▴ 10
2
votes
1
reply
657
views
Limma model orientation
limma methylation MethylationArray
updated 2.0 years ago by 65k • written 2.0 years ago by • 0
2
votes
2
replies
1.5k
views
dmrseq: cannot adjust for a covariate
dmrseq dmr dmrs bisulfite methylation
updated 6.2 years ago by ▴ 60 • written 6.3 years ago by • 0
2
votes
2
replies
871
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
9.6 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
1.4k
views
Skewed beta-distribution from Methylation EPIC array data
ChAMP EPIC Illumina Methylation
4.3 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
947
views
SVA paired samples
SVA EPIC methylation limma
updated 4.2 years ago by 65k • written 4.2 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
2.7k
views
bumphunter beta values
methylation minfi bumphunter
updated 8.1 years ago by 65k • written 8.1 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
824
views
Issue with ChAMP DMP.GUI
ChAMP champ methylation EPIC
updated 4.3 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
1.5k
views
Combining pfilter (wateRmelon) and preprocessNoob (minfi)
wateRmelon minfi methylation pfilter preprocessNoob
updated 4.7 years ago by ▴ 10 • written 4.7 years ago by • 0
1
vote
3
replies
1.0k
views
Differential methylation probes were much fewer than differential methylation genes
methylation limma
updated 4.5 years ago by 65k • written 4.5 years ago by • 0
1
vote
2
replies
1.4k
views
Methylation data visualization using methyAnalysis with minfi
methylation microarray illumina minfi methyanalysis
updated 5.4 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
2.0k
views
Extracting gene structures from a GFF3 file for use with annotateWithGeneParts()
genomicfeatures genomation genomicranges methylation annotation
updated 5.8 years ago by ▴ 20 • written 5.8 years ago by • 0
1
vote
0
replies
1.7k
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 6.0 years ago by 65k • written 6.0 years ago by ▴ 10
1
vote
4
replies
1.5k
views
dmrseq error: promise already under evaluation??
dmrseq Methylation
updated 4.9 years ago by ▴ 60 • written 4.9 years ago by • 0
1
vote
2
replies
1.5k
views
minfi package QC report error?
minfi methylation illumina
9.6 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 9.2 years ago by ▴ 80 • written 9.2 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 7.1 years ago by 65k • written 7.1 years ago by ▴ 10
1
vote
9
replies
3.6k
views
strange results from differential methylation analysis using limma
limma methylation methyanalysis IMA
updated 24 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 ▴ 180 • written 6.9 years ago by • 0
1
vote
3
replies
1.5k
views
Minfi returning incorrect beta values
minfi illumina illumina450k methylation R
6.8 years ago ezrabekele17 • 0
50 results • Page 1 of 1
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Comment: Couldn't connect to server while using "pathways" by ATpoint ★ 4.1k
Please understand that we neither can see your screen, nor read minds. You at least need to provide the line of code and the name of the pa…
Answer: Method to find pathways different between 2 groups by Gordon Smyth 50k
> When I search camera limma on pubmed, I found 2 papers I am unclear what point you are trying to make. limma's camera method has been fo…
Comment: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
limma most certainly is available. It installs in R 4.4.0 and Bioc 3.19 for all platforms without any issues. It has not had any period of …
Comment: package goseq seems to be not available on the latest version of R by Patrycja ▴ 20
limma package also isn't available.Is there any information when these packages will be available?
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 41k
Check the number of bootstrapped data per chromosome compared to the original, and then you can also look at its distribution. For this it'…
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Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Handling multiple differential expression comparisons
Answer: fgsea significant result
Answer: fgsea significant result
package goseq seems to be not available on the latest version of R
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