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champ
•
reset
0
votes
0
replies
18
views
Error in champ.load(): The following specified files do not exist
ChAMP
7 hours ago
Sherin
• 0
0
votes
0
replies
59
views
Cell type in SVD analysis
ChAMP
5 days ago
simleopold11
• 0
2
votes
6
replies
1.2k
views
How to get DMR for Infinium methylation EPIC v2
ChAMP
DMRcate
minfi
updated 14 days ago by
Tim Peters
▴ 170 • written 4 months ago by
rae.alshammari
▴ 10
1
vote
1
reply
250
views
Need Advice: Issue with ChAMP Analysis - Meth and UnMeth Matrix Pairing Error
MethylationArray
methylationArrayAnalysis
ChAMP
updated 7 weeks ago by
James W. MacDonald
65k • written 7 weeks ago by
david.cheishvili
• 0
0
votes
0
replies
177
views
how to solve this error?
ChAMPdata
ChAMP
8 weeks ago
Meghana
• 0
0
votes
2
replies
540
views
ChAMP - obtaining beta values using EPICv2 annotation
ChAMP
EPICv2
updated 10 weeks ago by
shuo
• 0 • written 3 months ago by
ChunkyJones
• 0
0
votes
0
replies
137
views
champ.load() from .idat files of GDC/TCGA dataset
TCGAbiolinks
ChAMP
10 weeks ago
Thalita
• 0
0
votes
7
replies
601
views
Deleted:No significant MVPs with a BH adjusted P-value below 0.05
ChAMP
updated 4 months ago by
Basti
▴ 760 • written 4 months ago by
486342583
• 0
2
votes
1
reply
557
views
ChAMP can't be found in Bioc3.18?
ChAMP
5 months ago
ramonfallon
▴ 20
0
votes
7
replies
1.8k
views
error with champ.load
ChAMP
champ
methylation
updated 8 months ago by
mike
• 0 • written 4.0 years ago by
jkong
• 0
0
votes
3
replies
610
views
ChAMP trouble reading csv file
ChAMP
written 8 months ago by
Keasiykan
• 0
1
vote
7
replies
1.7k
views
Error using champ.import
ChAMP
EPICv2
updated 12 hours ago by
shilpa
• 0 • written 9 months ago by
medha.suman
• 0
1
vote
16
replies
3.2k
views
error in ChAMP loading file
ChAMP
updated 5 weeks ago by
hortense96
• 0 • written 17 months ago by
Giulia
• 0
3
votes
7
replies
5.4k
views
error with champ.load
champ
written 6.5 years ago by
o.giannakopoulou
▴ 10
0
votes
2
replies
1.2k
views
Trouble Loading Data into Champ
loaddata
ChAMPdata
champload
R
ChAMP
updated 10 months ago by
hfbarrerat
• 0 • written 3.1 years ago by
Bethan
• 0
0
votes
3
replies
699
views
Error in champ.load() function
ChAMP
updated 11 months ago by
James W. MacDonald
65k • written 11 months ago by
Monalisa
• 0
0
votes
2
replies
678
views
How to find probe enhancer annotation for Illumina EPIC array?
IlluminaHumanMethylationEPICmanifest
ChAMP
annotation
updated 11 months ago by
James W. MacDonald
65k • written 11 months ago by
Matilda
• 0
0
votes
2
replies
981
views
Error in loading file using champ.load() from ChAMP package
champ.load
epicarray
ChAMP
methylationArrayAnalysis
12 months ago • updated 11 months ago
arisarkar88
▴ 40
2
votes
5
replies
1.8k
views
Problem at champ.load
ChAMPdata
ChAMP
updated 5 weeks ago by
James W. MacDonald
65k • written 12 months ago by
angel
• 0
0
votes
0
replies
568
views
Unable to create pd file for ChAMP analysis
ChAMP
12 months ago
Monalisa
• 0
0
votes
0
replies
378
views
Cannot generate plots when calling ChAMP
ChAMP
DMP.GUI
12 months ago
Kan
• 0
0
votes
2
replies
725
views
error in champ.SVD
svd
methylation
champ
updated 12 months ago by
shepherl
3.8k • written 12 months ago by
Giulia
• 0
0
votes
3
replies
1.3k
views
ChAMP filter bug when using beta matrix and pd as input
ChAMP
written 6.8 years ago by
allenyuchishing
• 0
1
vote
1
reply
711
views
champ.load IDAT files from subdirectories
ChAMP
updated 13 months ago by
Basti
▴ 760 • written 13 months ago by
Sin
• 0
0
votes
1
reply
1.1k
views
Trying to generate a pd file for ChAMP from idat files with no array or slide information in file names
ChAMP
updated 16 months ago by
James W. MacDonald
65k • written 16 months ago by
minardsmitha
▴ 10
1
vote
1
reply
648
views
In readLines(csvfile)
pipeline
testdata
ChAMP
updated 16 months ago by
James W. MacDonald
65k • written 16 months ago by
luisfranciscoteves
• 0
0
votes
1
reply
533
views
Champ.impute - myLoad not found
ChAMP
updated 18 months ago by
Basti
▴ 760 • written 18 months ago by
JD
• 0
0
votes
3
replies
1.1k
views
methylated/unmethylated media threshold (EPIC assay)
IlluminaHumanMethylationEPICanno.ilm10b3.hg19
ChAMP
minfi
2.0 years ago • updated 23 months ago
ramonfallon
▴ 20
0
votes
1
reply
1.2k
views
champ.SVD() error, assumes standard class() function will return single string
ChAMP
updated 23 months ago by
Basti
▴ 760 • written 23 months ago by
ramonfallon
▴ 20
0
votes
7
replies
2.6k
views
ERROR happens when install "DSS" package
methylationArrayAnalysis
ChAMP
DMP
DSS
updated 17 months ago by
James W. MacDonald
65k • written 23 months ago by
16301050225
• 0
0
votes
4
replies
1.3k
views
Problem installing ChAMP package.
ChAMP
24 months ago
Yu-min
• 0
0
votes
1
reply
833
views
How to control for confounders in champ.DMP and champ.DMR?
ChAMP
updated 2.0 years ago by
Basti
▴ 760 • written 2.0 years ago by
l.milicic
• 0
0
votes
1
reply
770
views
Error in ChAMP GUI
ChAMP
shiny
ChAMPdata
updated 2.1 years ago by
anna.stanislawska
• 0 • written 2.1 years ago by
Mari
• 0
1
vote
2
replies
2.5k
views
Error using ChAMP SVD analysis
ChAMP
updated 13 months ago by
Seohyun
• 0 • written 2.8 years ago by
FWNL15
• 0
0
votes
0
replies
849
views
Error in champ.svd - function 'EstDimRMTv2' within champ.svd acting inconsistently?
minfiData
ChAMP
2.3 years ago
behr201
• 0
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
▴ 760 • written 2.3 years ago by
mariat
• 0
0
votes
0
replies
809
views
Problem loading Red channel idat files with champ.load
R
MethylationArrayData
ChAMP
2.4 years ago
Paulina
• 0
3
votes
4
replies
8.5k
views
Problem loading R packages on MacBook Pro
newpackage
ChAMP
updated 19 months ago by
Yi Ping
• 0 • written 2.4 years ago by
Brendon
• 0
0
votes
2
replies
831
views
problems opening ChAMP
ChAMP
updated 2.5 years ago by
Basti
▴ 760 • written 2.5 years ago by
AaVee
• 0
0
votes
1
reply
1.1k
views
error in champ.norm
champ.norm
ChAMP
updated 2.5 years ago by
Kevin Blighe
★ 3.9k • written 2.5 years ago by
yu
• 0
0
votes
0
replies
734
views
ChAMP.CNA analysis
CopyNumberPlots
ChAMP
CopyNumberVariation
CopyNumberVariationData
2.6 years ago
FWNL15
• 0
0
votes
2
replies
1.2k
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
2.7 years ago • updated 2.6 years ago
Jinyue
• 0
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
0
votes
6
replies
3.3k
views
Merge problems in R
methylationArrayAnalysis
ChAMP
MethylationArrayData
2.8 years ago
FWNL15
• 0
1
vote
1
reply
1.3k
views
How to solve the error in running champ.DMP()
ChAMP
updated 2.9 years ago by
Basti
▴ 760 • written 2.9 years ago by
Federica
▴ 10
2
votes
1
reply
1.0k
views
How to save results of each step from ChAMP pipeline?
Bioconductor
ChAMP
updated 2.9 years ago by
Yuan Tian
▴ 270 • written 2.9 years ago by
Federica
▴ 10
2
votes
1
reply
1.2k
views
How to download the ChAMP dependency ChAMPdata
ChAMP
ChAMPdata
updated 2.9 years ago by
shepherl
3.8k • written 2.9 years ago by
Federica
▴ 10
0
votes
2
replies
1.3k
views
champ.SVD() : Error in while (step == 0) { : missing value where TRUE/FALSE needed
methylationArrayAnalysis
EPICarray
ChAMP
Champ.SVD
3.0 years ago
arisarkar88
▴ 40
0
votes
2
replies
859
views
Error myDMP not found
Illumina
methylationArrayAnalysis
ChAMPdata
ChAMP
3.2 years ago
sissialva21
• 0
0
votes
11
replies
6.2k
views
ChAMP input: Beta Matrix?
champ
dmr analysis
updated 3.3 years ago by
坤
• 0 • written 8.1 years ago by
Shicheng Guo
• 0
50 results • Page
1 of 1
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Replies
Comment: FilterByExpr low counts with small sample size
by
Gordon Smyth
50k
As always, it helps to see code. Are you running `voom` or `voomLmFit`? Did you run `normLibSizes()` in edgeR prior to `voom`? Are you star…
Comment: Batch correction and repeated measures
by
Gordon Smyth
50k
In your code, it was clear that `expr.mat` was a matrix rather than a DGEList, so it has to be a count matrix. If you have a DGEList object…
Comment: Methylation Analysis experiment design using Limma
by
Gordon Smyth
50k
I don't analyse methylation arrays so cannot advise on specific limma settings for that type of data. Please follow the advice of the methy…
Comment: Light difference when using coef vs omit a group when compare 3 groups.
by
Chris
• 0
Hi Gordon, thank you so much for further guidance! I discussed this issue with doctor know about Alzheimer and they don't expect significan…
Comment: Single-Cell Data Simulation from Bulk RNA-seq
by
wichaidi
• 0
Hi - I am wondering what you decided to do. I am currently in a similar condition where I need to create a toy scRNAseq data from bulk.
Votes
Answer: How many of my genes from my gene list are in each KEGG pathway?
Comment: Light difference when using coef vs omit a group when compare 3 groups.
DESeq2 variance transformation error and plot dispersion Estimate
A: DESeq2 variance transformation error and plot dispersion Estimate
ensembl to hgnc symbols creates duplicates
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