Showing : ChAMP • reset
6
votes
2
replies
5.7k
views
What is logFC and "B" in methylation analysis ??
limma champ logfc
updated 8.3 years ago by ★ 28k • written 8.3 years ago by ▴ 60
4
votes
4
replies
3.0k
views
How to remove unwanted probes before normalization in 450k data
minfi 450k champ rnbeads
updated 8.2 years ago by 66k • written 8.2 years ago by ▴ 60
3
votes
4
replies
3.0k
views
Error while using champ.svd() function in subset of data
ChAMP methylationepic epicarray epigenomics
updated 6.7 years ago by ▴ 140 • written 6.7 years ago by ▴ 10
3
votes
7
replies
5.5k
views
error with champ.load
champ
written 6.6 years ago by ▴ 10
3
votes
6
replies
2.1k
views
could not find function "champ.load"
ChAMP champ 2.9.10 methylationepic
6.2 years ago david.ch • 0
3
votes
4
replies
8.8k
views
Problem loading R packages on MacBook Pro
newpackage ChAMP
updated 20 months ago by • 0 • written 2.5 years ago by • 0
3
votes
9
replies
3.8k
views
champ.runCombat is failing: "invalid 'row.names' length"
champ
5.8 years ago Gurkenkönig ▴ 10
3
votes
5
replies
2.2k
views
Why the LogFC and delta-beta value are different in ChAMP
DNAMethylation ChAMP
updated 3 months ago by • 0 • written 3.5 years ago by • 0
2
votes
4
replies
316
views
Error EPICv2 ChAMP
ChAMPdata IlluminaHumanMethylationEPICv2anno.20a1.hg38 ChAMP
updated 4 weeks ago by 66k • written 5 weeks ago by • 0
2
votes
3
replies
1.8k
views
ChAMP was installed and library in R, however, I can't use the function
champ
6.2 years ago doctorjiangtao ▴ 10
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 5.5 years ago by ▴ 290 • written 5.5 years ago by ▴ 10
2
votes
2
replies
1.3k
views
Champ.lasso error @ dmr.beta.means[,22:24]
ChAMP
updated 8.3 years ago by ▴ 30 • written 8.9 years ago by ▴ 10
2
votes
3
replies
1.6k
views
champ.impute doesn't update beta matrix
champ impute bioconductor
updated 7.2 years ago by ▴ 90 • written 7.2 years ago by ▴ 10
2
votes
1
reply
1.1k
views
How to save results of each step from ChAMP pipeline?
Bioconductor ChAMP
updated 3.0 years ago by ▴ 290 • written 3.0 years ago by ▴ 10
2
votes
5
replies
2.4k
views
DMRcate fails in ChAMP package
ChAMP
updated 7.2 years ago by ▴ 90 • written 7.2 years ago by ▴ 10
2
votes
3
replies
2.3k
views
Error in champ.load (v. 2.8.3)
champ ChAMP
updated 6.9 years ago by ▴ 90 • written 6.9 years ago by ▴ 10
2
votes
1
reply
684
views
ChAMP can't be found in Bioc3.18?
ChAMP
6 months ago ramonfallon ▴ 20
2
votes
6
replies
1.6k
views
How to get DMR for Infinium methylation EPIC v2
ChAMP DMRcate minfi
updated 7 weeks ago by ▴ 180 • written 6 months ago by ▴ 10
2
votes
1
reply
1.3k
views
How to download the ChAMP dependency ChAMPdata
ChAMP ChAMPdata
updated 3.0 years ago by 3.9k • written 3.0 years ago by ▴ 10
2
votes
3
replies
203
views
Problem installing ChAMP on a MacBook
ChAMP
updated 10 days ago by 3.9k • written 10 days ago by • 0
2
votes
7
replies
2.5k
views
Blood cell composition adjustment in methylation EPIC array: ChAMP
MethylationArray methylationArrayAnalysis ChAMP
updated 7 months ago by • 0 • written 3.5 years ago by ▴ 20
2
votes
4
replies
1.4k
views
bumphunter stalls on "Smoothing coefficients"
bumphunter ChAMP
updated 5.0 years ago by ▴ 290 • written 5.0 years ago by ▴ 10
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
5
replies
1.9k
views
Error in Champ for Bioconductor performing GSEA analysis on Methlayion array data
champ bioconductor methyaltion epic array
updated 5.3 years ago by • 0 • written 5.4 years ago by • 0
2
votes
5
replies
2.0k
views
Problem at champ.load
ChAMPdata ChAMP
updated 10 weeks ago by 66k • written 13 months ago by • 0
2
votes
16
replies
2.6k
views
Methylation EPIC array: ChAMP package-champ.load added probes?
methylation epic champ champ.load() Methylation array
updated 4.4 years ago by ▴ 290 • written 4.4 years ago by ▴ 20
1
vote
1
reply
1.5k
views
Error in champ.lasso of ChAMP Bioconductor package for Methylation 450k analysis
ChAMP
8.9 years ago junyupub • 0
1
vote
1
reply
365
views
Need Advice: Issue with ChAMP Analysis - Meth and UnMeth Matrix Pairing Error
MethylationArray methylationArrayAnalysis ChAMP
updated 3 months ago by 66k • written 3 months ago by • 0
1
vote
0
replies
1.4k
views
How to find DMRs using probe-lasso from ChAMP using minfi data
ChAMP minfi DMR dmr analysis lasso
8.6 years ago AST ▴ 60
1
vote
2
replies
2.6k
views
Error using ChAMP SVD analysis
ChAMP
updated 14 months ago by • 0 • written 2.9 years ago by • 0
1
vote
16
replies
3.4k
views
error in ChAMP loading file
ChAMP
updated 10 weeks ago by • 0 • written 18 months ago by • 0
1
vote
1
reply
1.4k
views
ChAMP probe.features displays only CHR and MAPINFO, and it entails epic data, whereas probe.features.epic does not exist
champ
8.0 years ago line.heylen ▴ 10
1
vote
2
replies
1.5k
views
Problem installing ChAMP package.
software error microarray champ methylation
updated 5.8 years ago by 25k • written 5.8 years ago by ▴ 10
1
vote
1
reply
1.4k
views
How to solve the error in running champ.DMP()
ChAMP
updated 3.0 years ago by ▴ 780 • written 3.0 years ago by ▴ 10
1
vote
1
reply
1.1k
views
How to suggest BiocViews tags for an existing package?
biocviews champ
8.7 years ago Peter Hickey ▴ 740
1
vote
4
replies
2.5k
views
New version of ChAMP can not proceed through champ.DMP
champ
6.8 years ago sarka.vorackova • 0
1
vote
1
reply
687
views
In readLines(csvfile)
pipeline testdata ChAMP
updated 17 months ago by 66k • written 17 months ago by • 0
1
vote
2
replies
188
views
Error in champ.load(): The following specified files do not exist
ChAMP
5 weeks ago Sherin • 0
1
vote
1
reply
849
views
champ.DMP finds different probes in A-vs-B and B-vs-A analysis
DifferentialMethylation ChAMP champ.DMP
updated 3.5 years ago by ▴ 290 • written 3.5 years ago by • 0
1
vote
1
reply
831
views
Issue with ChAMP DMP.GUI
ChAMP champ methylation EPIC
updated 4.4 years ago by ▴ 90 • written 4.4 years ago by • 0
1
vote
2
replies
1.9k
views
Manhattan plot from ChAMP data
champ plot manhattan plot
updated 7.2 years ago by ▴ 90 • written 7.2 years ago by ▴ 10
1
vote
2
replies
1.1k
views
ChAMP not handling 3+ levels in contrasts
champ
updated 4.7 years ago by ▴ 290 • written 4.7 years ago by • 0
1
vote
1
reply
1.2k
views
Batch Correction and Normalization for champ.CNA
bioconductor ChAMP copy number batch effect normalization
updated 7.2 years ago by ▴ 10 • written 7.2 years ago by • 0
1
vote
5
replies
2.3k
views
error while using champ.svd() function
champ
5.4 years ago sinha.puja ▴ 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
3
replies
2.8k
views
normalization combination of noob + BMIQ/Quantile
minfi bmiq noob preprocessQuantile champ
updated 3.7 years ago by 66k • written 3.7 years ago by ▴ 50
1
vote
3
replies
1.5k
views
Error biocLite() newest version of ChAMP
R bioclite champ
6.1 years ago rosa_hegi ▴ 10
1
vote
8
replies
2.8k
views
Error in Champ for Bioconductor analyzing Methlayion array data
champ bioconductor contrastmatrix compare.group
updated 5.4 years ago by ▴ 290 • written 5.4 years ago by • 0
1
vote
3
replies
2.2k
views
champ.DMP phenotypes and covariates
champ champ.dmp()
updated 6.6 years ago by ▴ 290 • written 6.6 years ago by ▴ 10
1
vote
2
replies
2.4k
views
Beta-matrix - Differential methylation analysis
ChAMP tutorial
6.1 years ago Dave Emir • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: How to add Ensembl ids after Pseudobulk analysis by DESeq2 by BioinfGuru ▴ 30
I would use biomaRt. This is what happens when annotation occurs to early. If possible I would run the DEG analysis on the original output…
Comment: Volcano plot of scRNA-seq data not "centered" by ATpoint ★ 4.2k
My comment was generic. If your experiment causes drastic shifts then the situation might be different. The advise is the same: Try to use …
Comment: conumee with Infinium MethylationEPIC v2.0 by Maximus • 0
Hi Sole, If there is a combined mixture of MSet of 450K, EPIC and EPICv2, how should I create an annotation object? I tried to create anno…
Comment: Volcano plot of scRNA-seq data not "centered" by tjl • 0
Thank you both. The code is below, simplified a bit for simplicity. ATpoint, your suggestion re: the top 20% of genes by baseMean makes me …
Comment: Cannot install oligo on Fedora by James W. MacDonald 66k
Wait a minute. The `oligo` package is *supposed to* be using `zlibbioc`, but apparently it is not. I get the same thing as you do, where it…
Votes
A: Analyzing data without replicates using DiffBind
A: Analyzing data without replicates using DiffBind
DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Gene symbol
DESeq2 swap ensembl gene id rownames with gene symbol column
A: DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Ge
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