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champ
•
reset
0
votes
3
replies
1.9k
views
Why the order of sample names in the beta matrix affect the analysis results of Champ.DMP? What should I do?
ChAMP
limma
Bioconductor
ChAMPdata
updated 8 months ago by
81becky
• 0 • written 4.2 years ago by
Jinyue
• 0
0
votes
5
replies
2.2k
views
Loading ChAMP IdatFiles with two different ArrayTypes
ChAMP
updated 4.2 years ago by
Yuan Tian
▴ 290 • written 4.2 years ago by
FWNL15
• 0
0
votes
6
replies
4.8k
views
Merge problems in R
methylationArrayAnalysis
ChAMP
MethylationArrayData
4.3 years ago
FWNL15
• 0
1
vote
1
reply
2.1k
views
How to solve the error in running champ.DMP()
ChAMP
updated 4.4 years ago by
Basti
▴ 780 • written 4.4 years ago by
Federica
▴ 10
2
votes
1
reply
1.5k
views
How to save results of each step from ChAMP pipeline?
Bioconductor
ChAMP
updated 4.4 years ago by
Yuan Tian
▴ 290 • written 4.4 years ago by
Federica
▴ 10
2
votes
1
reply
1.8k
views
How to download the ChAMP dependency ChAMPdata
ChAMP
ChAMPdata
updated 4.4 years ago by
shepherl
4.2k • written 4.4 years ago by
Federica
▴ 10
0
votes
2
replies
1.8k
views
champ.SVD() : Error in while (step == 0) { : missing value where TRUE/FALSE needed
methylationArrayAnalysis
EPICarray
ChAMP
Champ.SVD
4.5 years ago
arisarkar88
▴ 40
0
votes
2
replies
1.3k
views
Error myDMP not found
Illumina
methylationArrayAnalysis
ChAMPdata
ChAMP
4.7 years ago
sissialva21
• 0
0
votes
12
replies
8.1k
views
ChAMP input: Beta Matrix?
champ
dmr analysis
updated 15 months ago by
tahirah.yasmin2014
• 0 • written 9.6 years ago by
Shicheng Guo
• 0
0
votes
0
replies
770
views
ChAMP batch effect
ChAMP
4.8 years ago
SMA180043
• 0
1
vote
2
replies
1.5k
views
what is "sample_well" and "pool_ID" in ChAMP
ChAMP
4.8 years ago
Hongbii
• 0
2
votes
7
replies
3.7k
views
Blood cell composition adjustment in methylation EPIC array: ChAMP
MethylationArray
methylationArrayAnalysis
ChAMP
updated 2.0 years ago by
dorota.komar
• 0 • written 4.9 years ago by
Ankit
▴ 20
3
votes
5
replies
3.3k
views
Why the LogFC and delta-beta value are different in ChAMP
DNAMethylation
ChAMP
updated 20 months ago by
sup0903
• 0 • written 4.9 years ago by
Hongbii
• 0
1
vote
1
reply
1.2k
views
champ.DMP finds different probes in A-vs-B and B-vs-A analysis
DifferentialMethylation
ChAMP
champ.DMP
updated 4.9 years ago by
Yuan Tian
▴ 290 • written 4.9 years ago by
Ricardo
• 0
1
vote
3
replies
4.0k
views
normalization combination of noob + BMIQ/Quantile
minfi
bmiq
noob
preprocessQuantile
champ
updated 5.1 years ago by
James W. MacDonald
68k • written 5.1 years ago by
Lin
▴ 50
0
votes
1
reply
1.2k
views
the function DMR in ChAMP package
ChAMP
DMR
updated 5.4 years ago by
Yuan Tian
▴ 290 • written 5.4 years ago by
olive8306
• 0
0
votes
1
reply
1.0k
views
rebuild the ChAMP package
ChAMP
updated 5.6 years ago by
Martin Morgan
25k • written 5.6 years ago by
olive8306
• 0
0
votes
0
replies
723
views
ChAMP DMP col abbreviations stend for what?
ChAMP
5.6 years ago
julie
• 0
0
votes
1
reply
1.1k
views
about the ChAMP package, the champ.norm output different results,when run it twice on epic data.
ChAMP
updated 5.6 years ago by
Yuan Tian
▴ 290 • written 5.6 years ago by
olive8306
• 0
1
vote
3
replies
2.0k
views
Skewed beta-distribution from Methylation EPIC array data
ChAMP
EPIC
Illumina
Methylation
5.7 years ago
erwin.tomasich
▴ 10
1
vote
1
reply
1.2k
views
Issue with ChAMP DMP.GUI
ChAMP
champ
methylation
EPIC
updated 5.8 years ago by
Yuan Tian
▴ 90 • written 5.8 years ago by
cherlyn.t
• 0
2
votes
16
replies
4.2k
views
Methylation EPIC array: ChAMP package-champ.load added probes?
methylation
epic
champ
champ.load()
Methylation array
updated 5.8 years ago by
Yuan Tian
▴ 290 • written 5.8 years ago by
Ankit
▴ 20
1
vote
2
replies
1.5k
views
ChAMP not handling 3+ levels in contrasts
champ
updated 6.1 years ago by
Yuan Tian
▴ 290 • written 6.1 years ago by
ognjen011
• 0
0
votes
2
replies
1.8k
views
cpg.annotate model requirements
DMRcate
ChAMP
updated 6.2 years ago by
Yuan Tian
▴ 290 • written 6.2 years ago by
kadm
• 0
0
votes
1
reply
3.0k
views
Differential Methylation Analysis using ChAMP
ChAMP
updated 5 weeks ago by
Michael Love
43k • written 6.3 years ago by
learning.iq84
• 0
2
votes
4
replies
2.0k
views
bumphunter stalls on "Smoothing coefficients"
bumphunter
ChAMP
updated 6.4 years ago by
Yuan Tian
▴ 290 • written 6.4 years ago by
rasmus.rydbirk
▴ 10
0
votes
2
replies
2.8k
views
ChAMP::champ.norm Error in champ.BMIQ(beta[, x], design.v, sampleID = colnames(beta)[x], : task 1 failed - "only defined on a data frame with all…
ChAMP
methylation
BMIQ
updated 23 months ago by
peter.brederlo
• 0 • written 6.5 years ago by
moldach
▴ 20
2
votes
5
replies
2.4k
views
Error in Champ for Bioconductor performing GSEA analysis on Methlayion array data
champ
bioconductor
methyaltion
epic array
updated 6.7 years ago by
godai987654
• 0 • written 6.8 years ago by
erinkello
• 0
1
vote
8
replies
3.7k
views
Error in Champ for Bioconductor analyzing Methlayion array data
champ
bioconductor
contrastmatrix
compare.group
updated 6.8 years ago by
Yuan Tian
▴ 290 • written 6.8 years ago by
erinkello
• 0
1
vote
5
replies
2.9k
views
error while using champ.svd() function
champ
6.8 years ago
sinha.puja
▴ 10
0
votes
3
replies
2.1k
views
ChAMP Methylation analysis error code "could not find function champ.load"
champ
6.8 years ago
sinha.puja
▴ 10
2
votes
1
reply
1.8k
views
EPIC methylation array - analysis with ChAMP - how to export bed/wig file to view in UCSC/IGV?
methylation
epic
champ
updated 6.9 years ago by
Yuan Tian
▴ 290 • written 6.9 years ago by
D
▴ 10
0
votes
2
replies
1.4k
views
How can I define which samples are controls and which samples are cases in ChAMP
ChAMP
champ.DMP
Cases
Controls
references
7.0 years ago
yuabrahamliu
• 0
0
votes
2
replies
2.2k
views
Use ChAMP to Find Differential Methylation Regions (DMR)
ChAMP
DMR
champ.DMR
7.0 years ago
yuabrahamliu
• 0
0
votes
2
replies
2.5k
views
Some terms in EPIC Methylation Analysis
ChAMP
SVD
Array
Slide
Sample Plate
updated 7.0 years ago by
Yuan Tian
▴ 290 • written 7.0 years ago by
yuabrahamliu
• 0
0
votes
2
replies
2.8k
views
ChAMP Normalization on EPIC Methylation Data
ChAMP
Normalization
FunctionalNormalization
methylation
EPIC
7.0 years ago
yuabrahamliu
• 0
0
votes
4
replies
1.7k
views
Taking relatedness among individuals into account in differential methylation analysis?
methylation
minfi
ChAMP
updated 7.2 years ago by
Kasper Daniel Hansen
★ 6.5k • written 7.2 years ago by
elgomez
• 0
0
votes
5
replies
3.0k
views
DNA methylation analysis without raw data IDAT files
r
illimina 450k methylation
minfi
champ
tcga
updated 7.2 years ago by
Yuan Tian
▴ 290 • written 7.2 years ago by
Beginner
▴ 60
1
vote
2
replies
1.9k
views
Problem installing ChAMP package.
software error
microarray
champ
methylation
updated 7.2 years ago by
Martin Morgan
25k • written 7.2 years ago by
cawten
▴ 10
3
votes
9
replies
4.6k
views
champ.runCombat is failing: "invalid 'row.names' length"
champ
7.2 years ago
Gurkenkönig
▴ 10
0
votes
1
reply
1.2k
views
Help with Errors in DMRcate ChAMP package
champ
7.2 years ago
urvi
• 0
0
votes
0
replies
793
views
ChAMP results interpretation
champ
7.3 years ago
Giovanni Calice
▴ 160
0
votes
1
reply
2.1k
views
install ChAMP under Ubuntu 18.04 in R 3.4.4 with error "maximal number of DLLs reached..."
ChAMP
software error
installation
7.4 years ago
chxp
• 0
0
votes
3
replies
1.9k
views
QC and normalization of 450K data from CSVs instead of IDATs
450K
CSV
normalization
minfi
ChAMP
updated 7.4 years ago by
Yuan Tian
▴ 290 • written 7.4 years ago by
Simone
▴ 190
0
votes
3
replies
1.6k
views
Error when running ChAMP package
champ
7.4 years ago
hazel.rogers
• 0
0
votes
1
reply
1.7k
views
ChAMP functional normalization error "subscript out of bounds"
champ
epic microarray
normalization
minfi
7.4 years ago
Laura
• 0
1
vote
3
replies
1.9k
views
Error biocLite() newest version of ChAMP
R
bioclite
champ
7.5 years ago
rosa_hegi
▴ 10
1
vote
2
replies
3.3k
views
Beta-matrix - Differential methylation analysis
ChAMP
tutorial
7.5 years ago
Dave Emir
• 0
0
votes
1
reply
1.1k
views
ChAMP error while lazyloading the latest version ChAMP_2.9.10
ChAMP
updated 7.5 years ago by
Yuan Tian
▴ 290 • written 7.5 years ago by
yura.grabovska
▴ 30
2
votes
3
replies
3.2k
views
"Seems your IDAT file not from one Array"
EPIC
methylation
ChAMP
updated 7.5 years ago by
yura.grabovska
▴ 30 • written 7.5 years ago by
david.ch
• 0
156 results • Page
2 of 4
Recent ...
Replies
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…
Comment: NA values for DESeq2 p-values and adjusted p-values using large sample sizes
by
Gabriel
• 0
Thank you very much for the reply. However, none of these three options seems to fit: 1) The genes for which NA appears do not have all 0 …
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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