Showing : 450K • reset
4
votes
10
replies
5.1k
views
Illumina MethylationEPIC vs. 450K
methylumi minfi illuminahumanmethylation450k.db 450k methyanalysis
updated 9.1 years ago by ▴ 750 • written 9.1 years ago by ▴ 50
1
vote
7
replies
4.2k
views
Loading beta values into minfi
minfi 450k
updated 9.4 years ago by ★ 6.5k • written 9.4 years ago by ▴ 10
3
votes
6
replies
2.3k
views
Minfi can't combineArrays
RGset combinearrays 450k minfi
updated 3.6 years ago by 68k • written 3.6 years ago by • 0
0
votes
6
replies
7.1k
views
ComBat with multiple batches
sva combat 450k
9.2 years ago ben.run974 • 0
1
vote
6
replies
2.6k
views
Reading 450k data in minfi
450K minfi
updated 6.0 years ago by • 0 • written 6.1 years ago by • 0
4
votes
4
replies
3.6k
views
How to remove unwanted probes before normalization in 450k data
minfi 450k champ rnbeads
updated 9.0 years ago by 68k • written 9.0 years ago by ▴ 60
0
votes
4
replies
2.0k
views
Use of confounders in downstream analysis
limma GSA confounding within-pair analysis 450k
9.9 years ago Aileen Bahl ▴ 10
0
votes
4
replies
2.9k
views
preprocessFunnorm in minfi
minfi 450k illuminahumanmethylation450k.db normalization
updated 9.3 years ago by 68k • written 9.3 years ago by • 0
3
votes
3
replies
3.7k
views
Adjustment of covariates in 450k data using Limma
limma covariates 450k
9.0 years ago AST ▴ 60
6
votes
3
replies
3.7k
views
Limma on Methylation Data - Fold Change Question
limma 450k
updated 9.7 years ago by ★ 28k • written 9.7 years ago by ▴ 370
0
votes
3
replies
1.8k
views
QC and normalization of 450K data from CSVs instead of IDATs
450K CSV normalization minfi ChAMP
updated 6.8 years ago by ▴ 290 • written 6.8 years ago by ▴ 190
0
votes
3
replies
1.5k
views
Limma for cell components effect on response
450k EPIC minfi limma cell components
updated 5.7 years ago by ★ 28k • written 5.7 years ago by • 0
6
votes
3
replies
12k
views
Minfi issue: return code from pthread_create() is 22
minfi 450k
updated 2.0 years ago by • 0 • written 5.7 years ago by ▴ 10
1
vote
2
replies
2.1k
views
QC/normalization standards for cancer studies with 450k array data
minfi watermelon cancer 450k normalization
updated 9.7 years ago by ★ 6.5k • written 9.7 years ago by ▴ 10
0
votes
2
replies
2.4k
views
Error using Bumphunter and Block finder using CHAMP
champ methylation 450k
8.3 years ago hrishi27n ▴ 20
0
votes
2
replies
2.1k
views
Loading RData files into ChAMP
microarray champ 450k
updated 9.5 years ago by • 0 • written 9.5 years ago by ▴ 10
6
votes
2
replies
5.1k
views
Plotting Differentially Methylated Regions
minfi bumphunter 450k region
updated 8.3 years ago by ▴ 80 • written 9.0 years ago by ▴ 40
1
vote
2
replies
2.6k
views
Bias correction for enrichment analysis of 450k methylation data => feed bias adjusted genes into IPA
goseq 450k enrichment
updated 10.1 years ago by ▴ 40 • written 10.1 years ago by ▴ 10
3
votes
1
reply
1.5k
views
two 450K methylation array manifests. where is the difference?
methylation 450k
9.1 years ago Pablo marin-garcia ▴ 90
0
votes
1
reply
4.7k
views
methyAnalysis M values and Beta Values
methyAnalysis methyanalysis 450k
updated 10.0 years ago by ▴ 80 • written 10.0 years ago by ▴ 370
0
votes
1
reply
2.5k
views
How to analyse 450k and EPIC methylation data together?
minfi 450k EPIC analysis
updated 5.6 years ago by 68k • written 5.6 years ago by • 0
2
votes
1
reply
1.9k
views
Minfi: estimateCellCounts rgSet
minfi 450k flowsorted.blood.450k
updated 8.3 years ago by ▴ 200 • written 9.0 years ago by ▴ 40
0
votes
1
reply
2.3k
views
News: Bug in ChAMP package champ.SVD() function
champ methylation 450k SVD EPIC News
8.6 years ago Yuan Tian ▴ 90
0
votes
0
replies
1.4k
views
Error when using Champ.SVD() function
champ champs.svd() 450K illimina 450k methylation champ 2.8.9
7.5 years ago david.ch • 0
0
votes
0
replies
1.6k
views
minfi v1.14 through champ: read.450k error with file path name
minfi champ illumina 450k
9.6 years ago jeroen • 0
0
votes
0
replies
1.7k
views
News: ChAMP2 is online
epigenetics EPIC 450K ChAMP News
8.5 years ago Yuan Tian ▴ 90
0
votes
0
replies
1.3k
views
Error in assay colnames when using readGEORawFile function in "minfi" package
minfi methylation 450k
8.3 years ago moonkinwen • 0
0
votes
0
replies
1.6k
views
minfi estimateCellCounts normalized beta values adjusted for cell type
minfi 450k
7.8 years ago igor ▴ 50
0
votes
0
replies
1.6k
views
How can I do paired test on my Illumina 450k idat files with ChAMP package?
Illumina 450k ChAMP paired test
9.1 years ago walter_teng • 0
0
votes
0
replies
1.3k
views
how to analyze "Beta-score" and get CNVdata using Comunee
conumee CNV 450K
7.1 years ago bird.of.clockwise • 0
0
votes
0
replies
949
views
Error when trying to read in idat files in methylumi
methylumi 450k methylation methylome
5.2 years ago A ▴ 40
0
votes
0
replies
642
views
cpgCollapse error
450K blockfinder cpgCollapse minfi
24 months ago edward.esiribloom • 0
0
votes
0
replies
1.5k
views
Repetitive motifs on Illumina 450k derived sequences
illumina 450k motifs meme
9.2 years ago Gustavo Fernández Bayón ▴ 440
33 results • Page 1 of 1
Recent ...
Replies
Comment: Problem installing package TxDb.Mmusculus.UCSC.mm10.knownGene by Wolfgang RAFFELSBERGER ▴ 140
Yes, rtools4.4 is installed (and works for making my own packages)
Comment: Problem installing package TxDb.Mmusculus.UCSC.mm10.knownGene by Wolfgang RAFFELSBERGER ▴ 140
Thank you, this solved the problem !
Comment: Problem installing package TxDb.Mmusculus.UCSC.mm10.knownGene by ATpoint ★ 4.7k
I cannot reproduce this on Windows 11. Is rtools installed to allow compilation from source on Windows?
Comment: Guidance Needed: Best Practices for Handling Technical Replicates in RNA-seq Ana by ATpoint ★ 4.7k
You've asked this at biostars where it belongs. This is not directly related to Bioconductor.
Comment: Conumee with EPICv2 Segment function by zpingfeng • 0
I have the same issue too for the analysis lack of sample replicates. It was fine for the samples with replicates
Votes
Comment: Identifying potentially associated gene set to drug response using GSVA
Answer: Limma - Complex 2-way multi-level contrast with paired samples
Comment: Can't post a question?
Answer: Limma - Complex 2-way multi-level contrast with paired samples
Answer: [ChIP-seq] DESeq2 on counts matrix from union set of called peaks
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