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CHAMP
•
reset
2
votes
16
replies
2.4k
views
Methylation EPIC array: ChAMP package-champ.load added probes?
methylation
epic
champ
champ.load()
Methylation array
updated 4.2 years ago by
Yuan Tian
▴ 270 • written 4.2 years ago by
Ankit
▴ 20
1
vote
16
replies
3.1k
views
error in ChAMP loading file
ChAMP
updated 17 days ago by
hortenseguillaume96
• 0 • written 16 months ago by
Giulia
• 0
0
votes
11
replies
6.1k
views
ChAMP input: Beta Matrix?
champ
dmr analysis
updated 3.2 years ago by
坤
• 0 • written 8.1 years ago by
Shicheng Guo
• 0
3
votes
9
replies
3.7k
views
champ.runCombat is failing: "invalid 'row.names' length"
champ
5.6 years ago
Gurkenkönig
▴ 10
0
votes
8
replies
1.4k
views
Error in running the ChAMP test runs from vignette
ChAMP
updated 7.4 years ago by
Yuan Tian
▴ 90 • written 7.4 years ago by
vd4mmind
• 0
1
vote
8
replies
2.7k
views
Error in Champ for Bioconductor analyzing Methlayion array data
champ
bioconductor
contrastmatrix
compare.group
updated 5.2 years ago by
Yuan Tian
▴ 270 • written 5.2 years ago by
erinkello
• 0
0
votes
7
replies
1.7k
views
error with champ.load
ChAMP
champ
methylation
updated 7 months ago by
mike
• 0 • written 4.0 years ago by
jkong
• 0
0
votes
7
replies
559
views
Deleted:No significant MVPs with a BH adjusted P-value below 0.05
ChAMP
updated 4 months ago by
Basti
▴ 750 • written 4 months ago by
486342583
• 0
0
votes
7
replies
2.5k
views
ERROR happens when install "DSS" package
methylationArrayAnalysis
ChAMP
DMP
DSS
updated 17 months ago by
James W. MacDonald
65k • written 22 months ago by
16301050225
• 0
2
votes
7
replies
2.3k
views
Blood cell composition adjustment in methylation EPIC array: ChAMP
MethylationArray
methylationArrayAnalysis
ChAMP
updated 5 months ago by
dorota.komar
• 0 • written 3.3 years ago by
Ankit
▴ 20
3
votes
7
replies
5.3k
views
error with champ.load
champ
written 6.4 years ago by
o.giannakopoulou
▴ 10
1
vote
6
replies
1.5k
views
Error using champ.import
ChAMP
EPICv2
updated 6 weeks ago by
fernanda.hackenhaa
• 0 • written 9 months ago by
medha.suman
• 0
0
votes
6
replies
1.6k
views
Errors with champ.block
champ
champ.block
6.3 years ago
tiroshamit
• 0
3
votes
6
replies
2.0k
views
could not find function "champ.load"
ChAMP
champ 2.9.10
methylationepic
6.0 years ago
david.ch
• 0
0
votes
6
replies
3.3k
views
Merge problems in R
methylationArrayAnalysis
ChAMP
MethylationArrayData
2.7 years ago
FWNL15
• 0
0
votes
6
replies
2.1k
views
ChAMP filter removing good samples from different batch of EPIC arrays.
minfi
champ
updated 6.6 years ago by
Yuan Tian
▴ 90 • written 6.7 years ago by
sarka.vorackova
• 0
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 5.2 years ago by
godai987654
• 0 • written 5.2 years ago by
erinkello
• 0
1
vote
5
replies
2.2k
views
error while using champ.svd() function
champ
5.3 years ago
sinha.puja
▴ 10
3
votes
5
replies
2.1k
views
Why the LogFC and delta-beta value are different in ChAMP
DNAMethylation
ChAMP
updated 5 weeks ago by
sup0903
• 0 • written 3.3 years ago by
Hongbii
• 0
2
votes
5
replies
2.3k
views
DMRcate fails in ChAMP package
ChAMP
updated 7.1 years ago by
Yuan Tian
▴ 90 • written 7.1 years ago by
rasmus.rydbirk
▴ 10
1
vote
5
replies
998
views
How to get DMR for Infinium methylation EPIC v2
ChAMP
DMRcate
minfi
updated 25 days ago by
James W. MacDonald
65k • written 4 months ago by
rae.alshammari
▴ 10
2
votes
5
replies
1.7k
views
Problem at champ.load
ChAMPdata
ChAMP
updated 17 days ago by
James W. MacDonald
65k • written 11 months ago by
angel
• 0
0
votes
5
replies
2.0k
views
DNA methylation analysis without raw data IDAT files
r
illimina 450k methylation
minfi
champ
tcga
updated 5.6 years ago by
Yuan Tian
▴ 270 • written 5.6 years ago by
Beginner
▴ 60
0
votes
5
replies
1.5k
views
Loading ChAMP IdatFiles with two different ArrayTypes
ChAMP
updated 2.7 years ago by
Yuan Tian
▴ 270 • written 2.7 years ago by
FWNL15
• 0
2
votes
4
replies
1.3k
views
bumphunter stalls on "Smoothing coefficients"
bumphunter
ChAMP
updated 4.9 years ago by
Yuan Tian
▴ 270 • written 4.9 years ago by
rasmus.rydbirk
▴ 10
1
vote
4
replies
2.3k
views
New version of ChAMP can not proceed through champ.DMP
champ
6.6 years ago
sarka.vorackova
• 0
0
votes
4
replies
1.1k
views
Taking relatedness among individuals into account in differential methylation analysis?
methylation
minfi
ChAMP
updated 5.6 years ago by
Kasper Daniel Hansen
★ 6.5k • written 5.6 years ago by
elgomez
• 0
0
votes
4
replies
1.3k
views
Problem installing ChAMP package.
ChAMP
23 months ago
Yu-min
• 0
3
votes
4
replies
2.9k
views
Error while using champ.svd() function in subset of data
ChAMP
methylationepic
epicarray
epigenomics
updated 6.5 years ago by
rcavalca
▴ 140 • written 6.5 years ago by
karthikrpad
▴ 10
4
votes
4
replies
2.9k
views
How to remove unwanted probes before normalization in 450k data
minfi
450k
champ
rnbeads
updated 8.0 years ago by
James W. MacDonald
65k • written 8.1 years ago by
AST
▴ 60
3
votes
4
replies
8.4k
views
Problem loading R packages on MacBook Pro
newpackage
ChAMP
updated 18 months ago by
Yi Ping
• 0 • written 2.4 years ago by
Brendon
• 0
1
vote
3
replies
1.5k
views
Error biocLite() newest version of ChAMP
R
bioclite
champ
6.0 years ago
rosa_hegi
▴ 10
0
votes
3
replies
1.4k
views
ChAMP Methylation analysis error code "could not find function champ.load"
champ
5.3 years ago
sinha.puja
▴ 10
0
votes
3
replies
1.1k
views
methylated/unmethylated media threshold (EPIC assay)
IlluminaHumanMethylationEPICanno.ilm10b3.hg19
ChAMP
minfi
24 months ago • updated 22 months ago
ramonfallon
▴ 20
0
votes
3
replies
565
views
ChAMP trouble reading csv file
ChAMP
written 8 months ago by
Keasiykan
• 0
0
votes
3
replies
1.9k
views
minfi release 1.8
SNP
Annotation
GO
probe
SNPlocs
PROcess
minfi
bumphunter
ChAMP
SNP
Annotation
GO
probe
updated 10.1 years ago by
Smeeta Shrestha
▴ 20 • written 10.2 years ago by
Tim Triche
★ 4.2k
0
votes
3
replies
1.1k
views
Error when running ChAMP package
champ
5.8 years ago
hazel.rogers
• 0
0
votes
3
replies
669
views
Error in champ.load() function
ChAMP
updated 10 months ago by
James W. MacDonald
65k • written 10 months ago by
Monalisa
• 0
0
votes
3
replies
1.8k
views
error in champ.DMR using DMRcate (v2.8.3)
champ
dmrcate
IlluminaHumanMethylationEPICanno.ilm10b2.hg19
updated 6.8 years ago by
Yuan Tian
▴ 90 • written 6.8 years ago by
mia
• 0
0
votes
3
replies
1.2k
views
ChAMP filter bug when using beta matrix and pd as input
ChAMP
written 6.8 years ago by
allenyuchishing
• 0
2
votes
3
replies
2.2k
views
Error in champ.load (v. 2.8.3)
champ
ChAMP
updated 6.8 years ago by
Yuan Tian
▴ 90 • written 6.8 years ago by
rasmus.rydbirk
▴ 10
0
votes
3
replies
1.2k
views
missing value in beta matrix after normalization wich champ.norm
champ
champs.svd()
champ.norm
6.1 years ago
jfertaj
▴ 30
2
votes
3
replies
1.6k
views
champ.impute doesn't update beta matrix
champ
impute
bioconductor
updated 7.0 years ago by
Yuan Tian
▴ 90 • written 7.0 years ago by
rasmus.rydbirk
▴ 10
0
votes
3
replies
7.5k
views
Downgrading R to an older version
MEDIPS
ChAMP
MEDIPS
ChAMP
updated 9.6 years ago by
Dan Tenenbaum
★ 8.2k • written 9.6 years ago by
Chong Kim San Allen
▴ 70
2
votes
3
replies
1.7k
views
ChAMP was installed and library in R, however, I can't use the function
champ
6.0 years ago
doctorjiangtao
▴ 10
0
votes
3
replies
1.0k
views
Wrong terminology used on champ.load() output of ChAMP package?
ChAMPdata
ChAMP
updated 2.3 years ago by
Basti
▴ 750 • written 2.3 years ago by
mariat
• 0
0
votes
3
replies
1.3k
views
QC and normalization of 450K data from CSVs instead of IDATs
450K
CSV
normalization
minfi
ChAMP
updated 5.8 years ago by
Yuan Tian
▴ 270 • written 5.8 years ago by
Simone
▴ 180
1
vote
3
replies
2.1k
views
champ.DMP phenotypes and covariates
champ
champ.dmp()
updated 6.4 years ago by
Yuan Tian
▴ 270 • written 6.4 years ago by
o.giannakopoulou
▴ 10
1
vote
3
replies
2.6k
views
normalization combination of noob + BMIQ/Quantile
minfi
bmiq
noob
preprocessQuantile
champ
updated 3.5 years ago by
James W. MacDonald
65k • written 3.5 years ago by
Lin
▴ 50
1
vote
3
replies
1.3k
views
Skewed beta-distribution from Methylation EPIC array data
ChAMP
EPIC
Illumina
Methylation
4.2 years ago
erwin.tomasich
▴ 10
50 results • Page
1 of 1
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Replies
Answer: Minfi - estimatecellscount
by
James W. MacDonald
65k
Don't filter first. You are likely removing the CpGs that are used to estimate the cell counts.
Comment: limma models out of memory issue on Slurm HPC
by
SamGG
▴ 330
> Alternatively you could run each linear model fit (var1 to var6) in a separate batch run, and again that would presumably work. I think …
Comment: fgsea fork
by
shepherl
3.8k
For What its worth BiocManager should also be able to install the github remotes `BiocManager::install("ctlab/fgsea")`
Comment: fgsea fork
by
alserg
▴ 240
I'm also not sure what you mean by fork, but you also can install the latest version of fgsea directly from GitHub with `devtools::install_…
Comment: limma models out of memory issue on Slurm HPC
by
Jitendra
▴ 10
thanks Gordon, but our methylation epic array input file is quite big and we can't read it in R by just using laptop memory so we need to …
Votes
transcript name mapping between human and mouse
transcript name mapping between human and mouse
A: Error object and replacement value dimnames differ, when changing column names o
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
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