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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
Aaron Lun
★ 28k • written 8.3 years ago by
AST
▴ 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
James W. MacDonald
65k • written 8.2 years ago by
AST
▴ 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
sup0903
• 0 • written 3.4 years ago by
Hongbii
• 0
3
votes
7
replies
5.4k
views
error with champ.load
champ
written 6.5 years ago by
o.giannakopoulou
▴ 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
rcavalca
▴ 140 • written 6.6 years ago by
karthikrpad
▴ 10
3
votes
4
replies
8.6k
views
Problem loading R packages on MacBook Pro
newpackage
ChAMP
updated 19 months ago by
Yi Ping
• 0 • written 2.5 years ago by
Brendon
• 0
2
votes
1
reply
586
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
shepherl
3.9k • written 3.0 years ago by
Federica
▴ 10
2
votes
2
replies
1.3k
views
Champ.lasso error @ dmr.beta.means[,22:24]
ChAMP
updated 8.2 years ago by
david.watson
▴ 30 • written 8.8 years ago by
zhourudy2
▴ 10
2
votes
3
replies
1.6k
views
champ.impute doesn't update beta matrix
champ
impute
bioconductor
updated 7.1 years ago by
Yuan Tian
▴ 90 • written 7.1 years ago by
rasmus.rydbirk
▴ 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
Yuan Tian
▴ 280 • written 4.3 years ago by
Ankit
▴ 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
Yuan Tian
▴ 280 • written 3.0 years ago by
Federica
▴ 10
2
votes
4
replies
1.4k
views
bumphunter stalls on "Smoothing coefficients"
bumphunter
ChAMP
updated 5.0 years ago by
Yuan Tian
▴ 280 • written 5.0 years ago by
rasmus.rydbirk
▴ 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
Yuan Tian
▴ 280 • written 5.5 years ago by
D
▴ 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
Tim Peters
▴ 180 • written 5 months ago by
rae.alshammari
▴ 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
dorota.komar
• 0 • written 3.4 years ago by
Ankit
▴ 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
Yuan Tian
▴ 90 • written 6.9 years ago by
rasmus.rydbirk
▴ 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
yura.grabovska
▴ 30 • written 6.1 years ago by
david.ch
• 0
2
votes
5
replies
2.3k
views
DMRcate fails in ChAMP package
ChAMP
updated 7.2 years ago by
Yuan Tian
▴ 90 • written 7.2 years ago by
rasmus.rydbirk
▴ 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
godai987654
• 0 • written 5.3 years ago by
erinkello
• 0
2
votes
5
replies
1.9k
views
Problem at champ.load
ChAMPdata
ChAMP
updated 7 weeks ago by
James W. MacDonald
65k • written 12 months ago by
angel
• 0
1
vote
16
replies
3.3k
views
error in ChAMP loading file
ChAMP
updated 7 weeks ago by
hortense96
• 0 • written 17 months ago by
Giulia
• 0
1
vote
2
replies
2.6k
views
Error using ChAMP SVD analysis
ChAMP
updated 14 months ago by
Seohyun
• 0 • written 2.8 years ago by
FWNL15
• 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
297
views
Need Advice: Issue with ChAMP Analysis - Meth and UnMeth Matrix Pairing Error
MethylationArray
methylationArrayAnalysis
ChAMP
updated 10 weeks ago by
James W. MacDonald
65k • written 10 weeks ago by
david.cheishvili
• 0
1
vote
2
replies
1.4k
views
Problem installing ChAMP package.
software error
microarray
champ
methylation
updated 5.7 years ago by
Martin Morgan
25k • written 5.7 years ago by
cawten
▴ 10
1
vote
2
replies
158
views
Error in champ.load(): The following specified files do not exist
ChAMP
18 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 3.0 years ago by
Basti
▴ 780 • written 3.0 years ago by
Federica
▴ 10
1
vote
4
replies
236
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
updated 14 days ago by
James W. MacDonald
65k • written 18 days ago by
Mirella Aurora
• 0
1
vote
7
replies
1.8k
views
Error using champ.import
ChAMP
EPICv2
updated 19 days ago by
shilpa
• 0 • written 10 months ago by
medha.suman
• 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
James W. MacDonald
65k • written 3.6 years ago by
Lin
▴ 50
1
vote
1
reply
824
views
Issue with ChAMP DMP.GUI
ChAMP
champ
methylation
EPIC
updated 4.3 years ago by
Yuan Tian
▴ 90 • written 4.3 years ago by
cherlyn.t
• 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
Yuan Tian
▴ 280 • written 4.6 years ago by
ognjen011
• 0
1
vote
2
replies
1.9k
views
Manhattan plot from ChAMP data
champ
plot
manhattan plot
updated 7.2 years ago by
Yuan Tian
▴ 90 • written 7.2 years ago by
rasmus.rydbirk
▴ 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
rasmus.rydbirk
▴ 10 • written 7.2 years ago by
apmishra
• 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
841
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
Yuan Tian
▴ 280 • written 3.4 years ago by
Ricardo
• 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
Yuan Tian
▴ 280 • written 5.3 years ago by
erinkello
• 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
2.2k
views
champ.DMP phenotypes and covariates
champ
champ.dmp()
updated 6.5 years ago by
Yuan Tian
▴ 280 • written 6.5 years ago by
o.giannakopoulou
▴ 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
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Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
I am working with mouse data. I don't know how to do this, but I will go through it. Can you help me with the second question? how do we …
Comment: [Mfuzz] Error in cmeans(exprs(eset)
by
Caio
• 0
You can have this problem (lines with variance equal to zero) when you run experiments and obtain the data with more samples and use fewer …
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
41k
The left plot indicates you should use genome segmentation. It is what is called "nonstationary" meaning it looks like there are distinct r…
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
gene_bioconductor
▴ 10
Thanks for your thoughtful and detailed comment, Gordon
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
I looked into the genomic distributions. Please see the screenshot attatched ![ distrubution for female loci, boot1 and boot2][1] how do …
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