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champ
•
reset
3
votes
6
replies
2.7k
views
could not find function "champ.load"
ChAMP
champ 2.9.10
methylationepic
7.6 years ago
david.ch
• 0
2
votes
3
replies
2.3k
views
ChAMP was installed and library in R, however, I can't use the function
champ
7.6 years ago
doctorjiangtao
▴ 10
0
votes
2
replies
2.0k
views
Error in champ.CNA (v. 2.6.0)
champ
updated 7.6 years ago by
elmori
• 0 • written 8.6 years ago by
rasmus.rydbirk
▴ 10
0
votes
3
replies
1.8k
views
missing value in beta matrix after normalization wich champ.norm
champ
champs.svd()
champ.norm
7.6 years ago
jfertaj
▴ 30
0
votes
1
reply
2.4k
views
ChAMP Methylation analysis error code "could not find function champ.load"
champ
methylationepic
updated 7.7 years ago by
Yuan Tian
▴ 290 • written 7.7 years ago by
csappleby-mallinder1
• 0
0
votes
2
replies
1.4k
views
error when using M-values in ChAMP
ChAMP
updated 19 months ago by
hortense96
• 0 • written 7.7 years ago by
a.mcneill
• 0
0
votes
2
replies
2.5k
views
Error code using ChAMP/Bioconductor, unable to load data from EPIC methylation array
bioconductor
methylation
epic microarray
champ
7.8 years ago
csappleby-mallinder1
• 0
0
votes
6
replies
2.3k
views
Errors with champ.block
champ
champ.block
7.9 years ago
tiroshamit
• 0
1
vote
3
replies
2.9k
views
champ.DMP phenotypes and covariates
champ
champ.dmp()
updated 8.0 years ago by
Yuan Tian
▴ 290 • written 8.0 years ago by
o.giannakopoulou
▴ 10
0
votes
0
replies
1.5k
views
Error when using Champ.SVD() function
champ
champs.svd()
450K
illimina 450k methylation
champ 2.8.9
8.1 years ago
david.ch
• 0
3
votes
4
replies
3.9k
views
Error while using champ.svd() function in subset of data
ChAMP
methylationepic
epicarray
epigenomics
updated 8.1 years ago by
rcavalca
▴ 140 • written 8.1 years ago by
karthikrpad
▴ 10
0
votes
2
replies
1.4k
views
Analysis of DNA hydroxymethylation
champ
minf
oxyBS
oxBS-MLE
updated 8.1 years ago by
Yuan Tian
▴ 90 • written 8.1 years ago by
sarka.vorackova
• 0
1
vote
4
replies
3.1k
views
New version of ChAMP can not proceed through champ.DMP
champ
8.2 years ago
sarka.vorackova
• 0
0
votes
6
replies
2.9k
views
ChAMP filter removing good samples from different batch of EPIC arrays.
minfi
champ
updated 8.2 years ago by
Yuan Tian
▴ 90 • written 8.2 years ago by
sarka.vorackova
• 0
0
votes
3
replies
2.5k
views
error in champ.DMR using DMRcate (v2.8.3)
champ
dmrcate
IlluminaHumanMethylationEPICanno.ilm10b2.hg19
updated 8.3 years ago by
Yuan Tian
▴ 90 • written 8.3 years ago by
mia
• 0
2
votes
3
replies
2.7k
views
Error in champ.load (v. 2.8.3)
champ
ChAMP
updated 8.3 years ago by
Yuan Tian
▴ 90 • written 8.3 years ago by
rasmus.rydbirk
▴ 10
0
votes
0
replies
1.6k
views
how to use Methylumi background correction (noob) in CHAMP
Methylumi
NOOB
CHAMP
Background corection
illimina 450k methylation
8.6 years ago
rahel14350
▴ 10
2
votes
3
replies
2.0k
views
champ.impute doesn't update beta matrix
champ
impute
bioconductor
updated 8.6 years ago by
Yuan Tian
▴ 90 • written 8.6 years ago by
rasmus.rydbirk
▴ 10
0
votes
1
reply
1.6k
views
champ.load getting filtered RGChannelSet
champ
methylation
updated 8.6 years ago by
Yuan Tian
▴ 90 • written 8.7 years ago by
Bioinformatician_R
▴ 20
1
vote
2
replies
2.5k
views
Manhattan plot from ChAMP data
champ
plot
manhattan plot
updated 8.6 years ago by
Yuan Tian
▴ 90 • written 8.6 years ago by
rasmus.rydbirk
▴ 10
2
votes
5
replies
3.0k
views
DMRcate fails in ChAMP package
ChAMP
updated 8.6 years ago by
Yuan Tian
▴ 90 • written 8.6 years ago by
rasmus.rydbirk
▴ 10
1
vote
1
reply
1.7k
views
Batch Correction and Normalization for champ.CNA
bioconductor
ChAMP
copy number
batch effect
normalization
updated 8.6 years ago by
rasmus.rydbirk
▴ 10 • written 8.6 years ago by
apmishra
• 0
0
votes
0
replies
1.3k
views
champ.CNA error (Error in sort(abs(diff(genomdat)))[1:n.keep])
ChAMP
champ
copy number
8.7 years ago
apmishra
• 0
0
votes
1
reply
2.0k
views
News:
Plotly uprading issue in ChAMP package
ChAMP
Epigenetics
plotly
Shiny
GUI
News
9.0 years ago • updated 8.8 years ago
Yuan Tian
▴ 90
0
votes
2
replies
1.1k
views
Bug: QC.GUI heatmap shows wrong column label order
ChAMP
8.8 years ago
berger
• 0
0
votes
2
replies
2.7k
views
Error using Bumphunter and Block finder using CHAMP
champ
methylation
450k
8.9 years ago
Bioinformatician_R
▴ 20
0
votes
1
reply
2.1k
views
Error while using ChAMP
champ
methylation
illuminahumanmethylation450k.db
illumina450k
updated 8.9 years ago by
Yuan Tian
▴ 90 • written 8.9 years ago by
Bioinformatician_R
▴ 20
0
votes
8
replies
1.9k
views
Error in running the ChAMP test runs from vignette
ChAMP
updated 9.0 years ago by
Yuan Tian
▴ 90 • written 9.0 years ago by
vd4mmind
• 0
0
votes
0
replies
1.8k
views
News:
ChAMP2 is online
epigenetics
EPIC
450K
ChAMP
News
9.0 years ago
Yuan Tian
▴ 90
0
votes
1
reply
2.5k
views
News:
Bug in ChAMP package champ.SVD() function
champ
methylation
450k
SVD
EPIC
News
9.1 years ago
Yuan Tian
▴ 90
0
votes
1
reply
2.8k
views
ChAMP error: "Error in density.default(beta1.v[class1.v == 1]) :need at least 2 points to select a bandwidth automatically..."
ChAMP
updated 9.2 years ago by
rl1385
• 0 • written 10.0 years ago by
jdangelo
• 0
0
votes
1
reply
1.5k
views
Error with IlluminaHumanMethylation450Kmanifest when trying to run ChAMP
ChAMP
illuminahumanmethylation450kmanifest
updated 9.3 years ago by
chaoqiang.lai
• 0 • written 9.3 years ago by
bohao.liu
• 0
0
votes
0
replies
1.8k
views
"error: C stack usage 265532545 is too close to the limit" with running ChAMP
ChAMP
9.4 years ago
chaoqiang.lai
• 0
1
vote
1
reply
1.7k
views
ChAMP probe.features displays only CHR and MAPINFO, and it entails epic data, whereas probe.features.epic does not exist
champ
9.4 years ago
line.heylen
▴ 10
0
votes
1
reply
1.2k
views
error when running champ.CNA command
ChAMP
updated 9.4 years ago by
AST
▴ 60 • written 9.4 years ago by
yuping.zhang
• 0
0
votes
0
replies
1.1k
views
I am getting a champ error during BatchNorm
ChAMP
illumina methylationepic 450k
9.4 years ago
brenna.hott
• 0
0
votes
0
replies
1.6k
views
ChAMP ComBat step error: Error in if (min(beta.c) == 0) { : missing value where TRUE/FALSE needed
ChAMP
methylation
illumina450k
9.4 years ago
Daniel E. Weeks
▴ 30
4
votes
4
replies
3.9k
views
How to remove unwanted probes before normalization in 450k data
minfi
450k
champ
rnbeads
updated 9.6 years ago by
James W. MacDonald
68k • written 9.6 years ago by
AST
▴ 60
0
votes
2
replies
1.7k
views
error running ChAMP vignette example
software error
champ
9.7 years ago
Hamid Bolouri
▴ 90
0
votes
0
replies
1.7k
views
How can I do paired test on my Illumina 450k idat files with ChAMP package?
Illumina
450k
ChAMP
paired test
9.7 years ago
walter_teng
• 0
2
votes
2
replies
1.6k
views
Champ.lasso error @ dmr.beta.means[,22:24]
ChAMP
updated 9.7 years ago by
david.watson
▴ 30 • written 10.3 years ago by
zhourudy2
▴ 10
7
votes
2
replies
7.0k
views
What is logFC and "B" in methylation analysis ??
limma
champ
logfc
updated 9.7 years ago by
Aaron Lun
★ 29k • written 9.7 years ago by
AST
▴ 60
0
votes
0
replies
1.5k
views
ChAMP MDS 1000 most variable positions
champ
MDS
9.8 years ago
Eric Smith
• 0
0
votes
0
replies
1.4k
views
ChAMP: champ.runCombat error
ChAMP
9.9 years ago
Brian Smith
▴ 120
0
votes
0
replies
1.5k
views
No significant MVPs with a BH adjusted P-value below 0.05
champ
mvp
9.9 years ago
maarten.caspers
• 0
0
votes
0
replies
2.0k
views
ChAMP: Error using champ.norm() function
ChAMP
methylation
epigenetics
10.0 years ago
jdangelo
• 0
1
vote
0
replies
1.6k
views
How to find DMRs using probe-lasso from ChAMP using minfi data
ChAMP
minfi
DMR
dmr analysis
lasso
10.0 years ago
AST
▴ 60
0
votes
2
replies
2.3k
views
Loading RData files into ChAMP
microarray
champ
450k
updated 10.0 years ago by
champ450k
• 0 • written 10.0 years ago by
CC
▴ 10
1
vote
1
reply
1.4k
views
How to suggest BiocViews tags for an existing package?
biocviews
champ
10.1 years ago
Peter Hickey
▴ 760
0
votes
0
replies
1.5k
views
Problem with lasso function (ChAMP package)
champ
lasso
10.1 years ago
AST
▴ 60
156 results • Page
3 of 4
Recent ...
Replies
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
dan.gatti
• 0
I am, but perhaps I'm not understanding how it should work. > sse = DropletUtils::read10xCounts(curr_files[1], mtx.class = 'SVT_Sparse…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
James W. MacDonald
68k
Did you use the development version as Aaron suggested? There is an argument to read the market matrix file directly into an `SVT_SparseMat…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
dan.gatti
• 0
Was anyone else able to put the pieces together using the reply above? I read in one 10X sample using DropletUtils::read10xCounts() and thi…
Comment: Announcing GBCC 2025: The first-ever joint conference between Bioconductor and G
by
dzv20413
• 0
Wow, GBCC 2025 sounds amazing, can not wait to see the logo contest results! Also, I just played [Level Devil][1] and it is super addictive…
Comment: Memory error while running alignments
by
Erik Wright
▴ 150
How much memory is available on the computer? A distance matrix of 50k sequences requires at least 50k*50k/2 * 8 bytes = 10GB, assuming the…
Votes
Comment: Check removeBatchEffect effectiveness
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset?
Answer: DESeq2 design for haplotype MPRA
A: Different logFC (log2foldchange) values for genes from limma-voom and other too
Comment: Check removeBatchEffect effectiveness
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