Showing : CHAMP • reset
6
votes
2
replies
5.6k
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
2.9k
views
How to remove unwanted probes before normalization in 450k data
minfi 450k champ rnbeads
updated 8.1 years ago by 65k • written 8.2 years ago by ▴ 60
3
votes
9
replies
3.7k
views
champ.runCombat is failing: "invalid 'row.names' length"
champ
5.7 years ago Gurkenkönig ▴ 10
3
votes
6
replies
2.1k
views
could not find function "champ.load"
ChAMP champ 2.9.10 methylationepic
6.1 years ago david.ch • 0
3
votes
5
replies
2.2k
views
Why the LogFC and delta-beta value are different in ChAMP
DNAMethylation ChAMP
updated 10 weeks ago by • 0 • written 3.4 years ago by • 0
3
votes
7
replies
5.4k
views
error with champ.load
champ
written 6.5 years ago by ▴ 10
3
votes
4
replies
3.0k
views
Error while using champ.svd() function in subset of data
ChAMP methylationepic epicarray epigenomics
updated 6.6 years ago by ▴ 140 • written 6.6 years ago by ▴ 10
3
votes
4
replies
8.6k
views
Problem loading R packages on MacBook Pro
newpackage ChAMP
updated 19 months ago by • 0 • written 2.5 years ago by • 0
2
votes
1
reply
582
views
ChAMP can't be found in Bioc3.18?
ChAMP
5 months ago ramonfallon ▴ 20
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
2
replies
1.3k
views
Champ.lasso error @ dmr.beta.means[,22:24]
ChAMP
updated 8.2 years ago by ▴ 30 • written 8.8 years ago by ▴ 10
2
votes
3
replies
1.6k
views
champ.impute doesn't update beta matrix
champ impute bioconductor
updated 7.1 years ago by ▴ 90 • written 7.1 years ago by ▴ 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
1
reply
1.0k
views
How to save results of each step from ChAMP pipeline?
Bioconductor ChAMP
updated 3.0 years ago by ▴ 280 • written 3.0 years ago by ▴ 10
2
votes
4
replies
1.4k
views
bumphunter stalls on "Smoothing coefficients"
bumphunter ChAMP
updated 5.0 years ago by ▴ 280 • written 5.0 years ago by ▴ 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 5.4 years ago by ▴ 280 • written 5.4 years ago by ▴ 10
2
votes
6
replies
1.4k
views
How to get DMR for Infinium methylation EPIC v2
ChAMP DMRcate minfi
updated 4 weeks ago by ▴ 180 • written 5 months ago by ▴ 10
2
votes
7
replies
2.4k
views
Blood cell composition adjustment in methylation EPIC array: ChAMP
MethylationArray methylationArrayAnalysis ChAMP
updated 6 months ago by • 0 • written 3.4 years ago by ▴ 20
2
votes
3
replies
1.7k
views
ChAMP was installed and library in R, however, I can't use the function
champ
6.1 years ago doctorjiangtao ▴ 10
2
votes
3
replies
2.2k
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
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
2.3k
views
DMRcate fails in ChAMP package
ChAMP
updated 7.2 years ago by ▴ 90 • written 7.2 years ago by ▴ 10
2
votes
5
replies
1.8k
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 5.3 years ago by • 0
2
votes
5
replies
1.9k
views
Problem at champ.load
ChAMPdata ChAMP
updated 7 weeks ago by 65k • written 12 months ago by • 0
1
vote
16
replies
3.3k
views
error in ChAMP loading file
ChAMP
updated 7 weeks ago by • 0 • written 17 months ago by • 0
1
vote
2
replies
2.6k
views
Error using ChAMP SVD analysis
ChAMP
updated 14 months ago by • 0 • written 2.8 years ago by • 0
1
vote
0
replies
1.3k
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
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
7.9 years ago line.heylen ▴ 10
1
vote
1
reply
1.4k
views
Error in champ.lasso of ChAMP Bioconductor package for Methylation 450k analysis
ChAMP
8.8 years ago junyupub • 0
1
vote
1
reply
290
views
Need Advice: Issue with ChAMP Analysis - Meth and UnMeth Matrix Pairing Error
MethylationArray methylationArrayAnalysis ChAMP
updated 10 weeks ago by 65k • written 10 weeks ago by • 0
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
2
replies
151
views
Error in champ.load(): The following specified files do not exist
ChAMP
16 days ago • updated 15 days ago Sherin • 0
1
vote
4
replies
2.4k
views
New version of ChAMP can not proceed through champ.DMP
champ
6.7 years ago sarka.vorackova • 0
1
vote
1
reply
1.3k
views
How to solve the error in running champ.DMP()
ChAMP
updated 2.9 years ago by ▴ 780 • written 3.0 years ago by ▴ 10
1
vote
4
replies
223
views
Error EPICv2 ChAMP
ChAMPdata IlluminaHumanMethylationEPICv2anno.20a1.hg38 ChAMP
updated 11 days ago by 65k • written 15 days ago by • 0
1
vote
7
replies
1.8k
views
Error using champ.import
ChAMP EPICv2
updated 16 days ago by • 0 • written 10 months ago by • 0
1
vote
3
replies
2.7k
views
normalization combination of noob + BMIQ/Quantile
minfi bmiq noob preprocessQuantile champ
updated 3.6 years ago by 65k • written 3.6 years ago by ▴ 50
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
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
1.1k
views
ChAMP not handling 3+ levels in contrasts
champ
updated 4.6 years ago by ▴ 280 • written 4.6 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
what is "sample_well" and "pool_ID" in ChAMP
ChAMP
3.4 years ago Hongbii • 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
1.5k
views
Error biocLite() newest version of ChAMP
R bioclite champ
6.1 years ago rosa_hegi ▴ 10
1
vote
1
reply
839
views
champ.DMP finds different probes in A-vs-B and B-vs-A analysis
DifferentialMethylation ChAMP champ.DMP
updated 3.4 years ago by ▴ 280 • written 3.4 years ago by • 0
1
vote
8
replies
2.8k
views
Error in Champ for Bioconductor analyzing Methlayion array data
champ bioconductor contrastmatrix compare.group
updated 5.3 years ago by ▴ 280 • written 5.3 years ago by • 0
1
vote
1
reply
1.1k
views
How to suggest BiocViews tags for an existing package?
biocviews champ
8.6 years ago Peter Hickey ▴ 740
1
vote
3
replies
2.1k
views
champ.DMP phenotypes and covariates
champ champ.dmp()
updated 6.5 years ago by ▴ 280 • written 6.5 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
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
You seem to have the misunderstanding that you can change the design matrix but keep all the other code unchanged. The contrasts are comput…
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0
Thank you Tim, this is a great help in getting me started!
Comment: Too many significant genes when integrating gtex and tcga by Michael Love 41k
Yes, this was one of the aspects we highlighted in the 2014 paper, and it's also in the workflow. Check these places first. Also take a st…
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
Awards • All
Popular Question to Gordon Smyth 50k
Popular Question to Zainab • 0
Popular Question to Theo ▴ 10
Popular Question to gene_bioconductor ▴ 10
Popular Question to rohitsatyam102 ▴ 20
Locations • All
WEHI, Melbourne, Australia, just now
France, 2 minutes ago
United States, 14 minutes ago
United States, 19 minutes ago
United States, 20 minutes ago
Traffic: 593 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