Showing : champ • reset
6
votes
2
replies
5.6k
views
What is logFC and "B" in methylation analysis ??
limma champ logfc
updated 8.2 years ago by ★ 28k • written 8.2 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 9 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
572
views
ChAMP can't be found in Bioc3.18?
ChAMP
5 months ago ramonfallon ▴ 20
2
votes
1
reply
1.2k
views
How to download the ChAMP dependency ChAMPdata
ChAMP ChAMPdata
updated 3.0 years ago by 3.8k • 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 27 days ago by ▴ 170 • 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 7.1 years ago by ▴ 90 • written 7.1 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
2.5k
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
277
views
Need Advice: Issue with ChAMP Analysis - Meth and UnMeth Matrix Pairing Error
MethylationArray methylationArrayAnalysis ChAMP
updated 9 weeks ago by 65k • written 9 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
141
views
Error in champ.load(): The following specified files do not exist
ChAMP
13 days ago • updated 12 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 2.9 years ago by ▴ 10
1
vote
4
replies
193
views
Error EPICv2 ChAMP
ChAMPdata IlluminaHumanMethylationEPICv2anno.20a1.hg38 ChAMP
updated 8 days ago by 65k • written 12 days ago by • 0
1
vote
7
replies
1.7k
views
Error using champ.import
ChAMP EPICv2
updated 13 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
821
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 7.1 years ago by ▴ 90 • written 7.1 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 7.1 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
835
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
2.3k
views
Beta-matrix - Differential methylation analysis
ChAMP tutorial
6.1 years ago Dave Emir • 0
50 results • Page 1 of 1
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Replies
Comment: Help with error using camera() in limma by Chris • 0
Thanks James! I fixed the error. I try gene symbol instead of entrez and it worked.
Comment: limma for gene expression analysis with big and unbalanced sample size by XW • 0
Could you explain more about the comment "there are no problems with using limma for unbalanced data sets" ? thanks.
Comment: Limma, eBayes different sample size of groups and adjustment by XW • 0
Could you explain more about how the analysis self-correct the different sample sizes when calling DEGs in limma? Thanks
Answer: How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy) by James W. MacDonald 65k
The section of the vignette that is *directly above the one you quote* says that you can use the HMMcopy utils to do all three things. And …
Comment: Help with error using camera() in limma by James W. MacDonald 65k
Again, this is where you need to read the help page and try to diagnose. It says ``` index: an index vector or a list of index vectors. …
Votes
C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB
C: Extremely big genes in annotation TxDb packages
Make custom Txdb class objects from Txdb
Comment: Help with error using camera() in limma
Answer: Help with error using camera() in limma
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