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ChAMP
•
reset
2
votes
10
replies
3.8k
views
Problem at champ.load
ChAMPdata
ChAMP
updated 5 days ago by
Josh
• 0 • written 23 months ago by
angel
• 0
0
votes
1
reply
414
views
ChAMP.DMR error - Error in makeGenomicRatioSetFromMatrix
ChAMP
updated 12 weeks ago by
O'Brien
• 0 • written 3 months ago by
André
• 0
0
votes
0
replies
293
views
Errors trying to load EPIC v2 data in ChAMP
ChAMP
ChAMPdata
4 months ago
elgomez
• 0
1
vote
9
replies
3.4k
views
Error using champ.import
ChAMP
EPICv2
updated 5 months ago by
Ricky
• 0 • written 21 months ago by
medha.suman
• 0
1
vote
1
reply
540
views
Empty Results from champ.DMP Despite Expected Output
MethylationArray
ChAMP
R
updated 6 months ago by
James W. MacDonald
68k • written 6 months ago by
Fateme
• 0
0
votes
4
replies
644
views
Failed to install geneLenDataBase
geneLenDataBase
ChAMP
updated 7 months ago by
shepherl
4.1k • written 7 months ago by
Fang
• 0
3
votes
12
replies
4.5k
views
How to get DMR for Infinium methylation EPIC v2
ChAMP
DMRcate
minfi
updated 8 months ago by
Tim Peters
▴ 230 • written 16 months ago by
rae.alshammari
▴ 10
0
votes
1
reply
672
views
ChAMP analysis Error: Meth Matrix and UnMeth Matrix seems not paried correctly AND incomplete final line
MethylationArray
methylationArrayAnalysis
ChAMP
updated 3 months ago by
nereaherrera23
• 0 • written 8 months ago by
Mathu
• 0
0
votes
1
reply
462
views
single excel file containing methylation beta values does not get loaded in ChAMP
ChAMP
updated 8 months ago by
Basti
▴ 780 • written 8 months ago by
tahirah.yasmin2014
• 0
0
votes
3
replies
1.5k
views
ChAMP not available for bioconductor 3.19
Bioconductor
ChAMP
updated 9 months ago by
shepherl
4.1k • written 10 months ago by
Macsue
• 0
2
votes
3
replies
858
views
Problem installing ChAMP on a MacBook
ChAMP
updated 10 months ago by
shepherl
4.1k • written 10 months ago by
Galia
• 0
0
votes
7
replies
1.4k
views
ChAMP installation issue
Cha
ChAMP
updated 10 months ago by
James W. MacDonald
68k • written 10 months ago by
e1271094
• 0
2
votes
4
replies
1.1k
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
updated 11 months ago by
James W. MacDonald
68k • written 11 months ago by
Mirella Aurora
• 0
1
vote
2
replies
524
views
Error in champ.load(): The following specified files do not exist
ChAMP
11 months ago
Sherin
• 0
1
vote
1
reply
1.4k
views
Need Advice: Issue with ChAMP Analysis - Meth and UnMeth Matrix Pairing Error
MethylationArray
methylationArrayAnalysis
ChAMP
updated 13 months ago by
James W. MacDonald
68k • written 13 months ago by
david.cheishvili
• 0
0
votes
0
replies
526
views
how to solve this error?
ChAMPdata
ChAMP
13 months ago
Meghana
• 0
0
votes
4
replies
2.8k
views
ChAMP - obtaining beta values using EPICv2 annotation
ChAMP
EPICv2
updated 4 months ago by
icecreamlover
• 0 • written 14 months ago by
ChunkyJones
• 0
0
votes
0
replies
511
views
champ.load() from .idat files of GDC/TCGA dataset
TCGAbiolinks
ChAMP
13 months ago
Thalita
• 0
0
votes
7
replies
1.3k
views
Deleted:No significant MVPs with a BH adjusted P-value below 0.05
ChAMP
updated 15 months ago by
Basti
▴ 780 • written 15 months ago by
486342583
• 0
2
votes
1
reply
1.1k
views
ChAMP can't be found in Bioc3.18?
ChAMP
16 months ago
ramonfallon
▴ 20
0
votes
7
replies
2.5k
views
error with champ.load
ChAMP
champ
methylation
updated 19 months ago by
mike
• 0 • written 5.0 years ago by
jkong
• 0
0
votes
3
replies
1.1k
views
ChAMP trouble reading csv file
ChAMP
written 20 months ago by
Keasiykan
• 0
1
vote
19
replies
5.4k
views
error in ChAMP loading file
ChAMP
updated 12 days ago by
shocked.tick.zyet
• 0 • written 2.3 years ago by
Giulia
• 0
3
votes
7
replies
6.6k
views
error with champ.load
champ
written 7.4 years ago by
o.giannakopoulou
▴ 10
0
votes
2
replies
1.7k
views
Trouble Loading Data into Champ
loaddata
ChAMPdata
champload
R
ChAMP
updated 22 months ago by
hfbarrerat
• 0 • written 4.1 years ago by
Bethan
• 0
0
votes
3
replies
1.0k
views
Error in champ.load() function
ChAMP
updated 22 months ago by
James W. MacDonald
68k • written 22 months ago by
Monalisa
• 0
0
votes
2
replies
1.4k
views
How to find probe enhancer annotation for Illumina EPIC array?
IlluminaHumanMethylationEPICmanifest
ChAMP
annotation
updated 22 months ago by
James W. MacDonald
68k • written 22 months ago by
Matilda
• 0
0
votes
2
replies
1.5k
views
Error in loading file using champ.load() from ChAMP package
champ.load
epicarray
ChAMP
methylationArrayAnalysis
23 months ago • updated 22 months ago
arisarkar88
▴ 40
0
votes
1
reply
969
views
Unable to create pd file for ChAMP analysis
ChAMP
updated 8 months ago by
tahirah.yasmin2014
• 0 • written 23 months ago by
Monalisa
• 0
0
votes
0
replies
586
views
Cannot generate plots when calling ChAMP
ChAMP
DMP.GUI
23 months ago
Kan
• 0
0
votes
2
replies
1.1k
views
error in champ.SVD
svd
methylation
champ
updated 23 months ago by
shepherl
4.1k • written 23 months ago by
Giulia
• 0
0
votes
3
replies
1.7k
views
ChAMP filter bug when using beta matrix and pd as input
ChAMP
written 7.8 years ago by
allenyuchishing
• 0
1
vote
1
reply
1.3k
views
champ.load IDAT files from subdirectories
ChAMP
updated 2.0 years ago by
Basti
▴ 780 • written 2.0 years ago by
Sin
• 0
0
votes
1
reply
1.8k
views
Trying to generate a pd file for ChAMP from idat files with no array or slide information in file names
ChAMP
updated 2.3 years ago by
James W. MacDonald
68k • written 2.3 years ago by
minardsmitha
▴ 10
1
vote
1
reply
980
views
In readLines(csvfile)
pipeline
testdata
ChAMP
updated 2.3 years ago by
James W. MacDonald
68k • written 2.3 years ago by
luisfranciscoteves
• 0
0
votes
1
reply
864
views
Champ.impute - myLoad not found
ChAMP
updated 2.5 years ago by
Basti
▴ 780 • written 2.5 years ago by
JD
• 0
0
votes
3
replies
1.6k
views
methylated/unmethylated media threshold (EPIC assay)
IlluminaHumanMethylationEPICanno.ilm10b3.hg19
ChAMP
minfi
3.0 years ago • updated 2.8 years ago
ramonfallon
▴ 20
0
votes
1
reply
1.6k
views
champ.SVD() error, assumes standard class() function will return single string
ChAMP
updated 2.8 years ago by
Basti
▴ 780 • written 2.8 years ago by
ramonfallon
▴ 20
0
votes
7
replies
3.5k
views
ERROR happens when install "DSS" package
methylationArrayAnalysis
ChAMP
DMP
DSS
updated 2.4 years ago by
James W. MacDonald
68k • written 2.9 years ago by
16301050225
• 0
0
votes
4
replies
1.8k
views
Problem installing ChAMP package.
ChAMP
2.9 years ago
Yu-min
• 0
0
votes
1
reply
1.3k
views
How to control for confounders in champ.DMP and champ.DMR?
ChAMP
updated 3.0 years ago by
Basti
▴ 780 • written 3.0 years ago by
l.milicic
• 0
0
votes
1
reply
1.1k
views
Error in ChAMP GUI
ChAMP
shiny
ChAMPdata
updated 3.0 years ago by
anna.stanislawska
• 0 • written 3.0 years ago by
Mari
• 0
1
vote
2
replies
3.4k
views
Error using ChAMP SVD analysis
ChAMP
updated 2.1 years ago by
Seohyun
• 0 • written 3.7 years ago by
FWNL15
• 0
0
votes
0
replies
1.2k
views
Error in champ.svd - function 'EstDimRMTv2' within champ.svd acting inconsistently?
minfiData
ChAMP
3.2 years ago
behr201
• 0
0
votes
3
replies
1.4k
views
Wrong terminology used on champ.load() output of ChAMP package?
ChAMPdata
ChAMP
updated 3.2 years ago by
Basti
▴ 780 • written 3.2 years ago by
mariat
• 0
0
votes
0
replies
1.1k
views
Problem loading Red channel idat files with champ.load
R
MethylationArrayData
ChAMP
3.3 years ago
Paulina
• 0
3
votes
4
replies
11k
views
Problem loading R packages on MacBook Pro
newpackage
ChAMP
updated 2.5 years ago by
Yi Ping
• 0 • written 3.4 years ago by
Brendon
• 0
0
votes
2
replies
1.1k
views
problems opening ChAMP
ChAMP
updated 3.4 years ago by
Basti
▴ 780 • written 3.4 years ago by
AaVee
• 0
0
votes
1
reply
1.4k
views
error in champ.norm
champ.norm
ChAMP
updated 3.5 years ago by
Kevin Blighe
★ 4.0k • written 3.5 years ago by
yu
• 0
0
votes
0
replies
1.0k
views
ChAMP.CNA analysis
CopyNumberPlots
ChAMP
CopyNumberVariation
CopyNumberVariationData
3.5 years ago
FWNL15
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: DiffBind custom normalization factor
by
Abbie
• 0
Hello! Thanks so much for adding dba.normalize and all the documentation in the manual! I'm hoping I can ask a follow-up question here. I…
Answer: CpGs with genomic positions greater than the chromosome size in EPICv2?
by
James W. MacDonald
68k
All of the annotation packages provided by Bioconductor are simply repackaging of existing data from one or more sources. In this case, the…
Comment: Using TPM from tximport of Salmon output for singscore
by
Kent
• 0
Thank you for the suggestions Michael. Would you say that after filtering out the low count genes, `rlog(counts, blind = T)` is doing the s…
Comment: Using TPM from tximport of Salmon output for singscore
by
Michael Love
43k
For clustering generally we recommend `vst()` see the workflow for example. For working with individual samples, I can see how a scaling/t…
Comment: DESeq2 model - How to test case/control time course model when taking account wi
by
Michael Love
43k
I'd recommend working with a local statistician or someone familiar with linear models in R. I have to reserve my time on the support site …
Votes
clusterProfiler-GO enrichment Error
A: Machine learning in R book
Data preparation and Machine learning on time course RNAseq data
Data preparation and Machine learning on time course RNAseq data
Answer: Use of org.Rn.eg.db with GRCr8 reference genome
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