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champ
•
reset
2
votes
10
replies
3.9k
views
Problem at champ.load
ChAMPdata
ChAMP
updated 17 days ago by
Josh
• 0 • written 23 months ago by
angel
• 0
0
votes
1
reply
431
views
ChAMP.DMR error - Error in makeGenomicRatioSetFromMatrix
ChAMP
updated 3 months ago by
O'Brien
• 0 • written 3 months ago by
André
• 0
0
votes
0
replies
301
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
568
views
Empty Results from champ.DMP Despite Expected Output
MethylationArray
ChAMP
R
updated 7 months ago by
James W. MacDonald
68k • written 7 months ago by
Fateme
• 0
0
votes
4
replies
655
views
Failed to install geneLenDataBase
geneLenDataBase
ChAMP
updated 8 months ago by
shepherl
4.1k • written 8 months ago by
Fang
• 0
4
votes
12
replies
4.7k
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
▴ 20
0
votes
1
reply
688
views
ChAMP analysis Error: Meth Matrix and UnMeth Matrix seems not paried correctly AND incomplete final line
MethylationArray
methylationArrayAnalysis
ChAMP
updated 4 months ago by
nereaherrera23
• 0 • written 9 months ago by
Mathu
• 0
0
votes
1
reply
475
views
single excel file containing methylation beta values does not get loaded in ChAMP
ChAMP
updated 9 months ago by
Basti
▴ 780 • written 9 months ago by
tahirah.yasmin2014
• 0
0
votes
3
replies
1.5k
views
ChAMP not available for bioconductor 3.19
Bioconductor
ChAMP
updated 10 months ago by
shepherl
4.1k • written 10 months ago by
Macsue
• 0
2
votes
3
replies
864
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
1.5k
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
1.2k
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
533
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
534
views
how to solve this error?
ChAMPdata
ChAMP
13 months ago
Meghana
• 0
0
votes
4
replies
2.9k
views
ChAMP - obtaining beta values using EPICv2 annotation
ChAMP
EPICv2
updated 4 months ago by
icecreamlover
• 0 • written 15 months ago by
ChunkyJones
• 0
0
votes
0
replies
520
views
champ.load() from .idat files of GDC/TCGA dataset
TCGAbiolinks
ChAMP
14 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 16 months ago by
Basti
▴ 780 • written 16 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
5.5k
views
error in ChAMP loading file
ChAMP
updated 25 days ago by
shocked.tick.zyet
• 0 • written 2.4 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 23 months ago by
James W. MacDonald
68k • written 23 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 23 months ago by
James W. MacDonald
68k • written 23 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
arisarkar88
▴ 40
0
votes
1
reply
983
views
Unable to create pd file for ChAMP analysis
ChAMP
updated 9 months ago by
tahirah.yasmin2014
• 0 • written 23 months ago by
Monalisa
• 0
0
votes
0
replies
589
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 24 months ago by
shepherl
4.1k • written 24 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 2.1 years ago by
Basti
▴ 780 • written 2.1 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
990
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
872
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 2.9 years ago
ramonfallon
▴ 20
0
votes
1
reply
1.6k
views
champ.SVD() error, assumes standard class() function will return single string
ChAMP
updated 2.9 years ago by
Basti
▴ 780 • written 2.9 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
3.0 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
1.2k
views
Error in ChAMP GUI
ChAMP
shiny
ChAMPdata
updated 3.1 years ago by
anna.stanislawska
• 0 • written 3.1 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 3.3 years ago by
Basti
▴ 780 • written 3.3 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
1.2k
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
3.6 years ago
FWNL15
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: DESeq2 - human data, weird results, troubleshooting
by
bd2000
▴ 30
I didn't include all of my code the post would be too long. Here's a link to my GitHub if anyone would like to see the full code: [Full Rst…
Answer: DESeq: Gene is not flagged as differentially expressed despite count data showin
by
James W. MacDonald
68k
The simple answer is that the within-group variability is much higher for the first gene as compared to the second. The Wald statistic is j…
Comment: DESeq: Gene is not flagged as differentially expressed despite count data showin
by
ATpoint
★ 4.8k
> since there doesn't seem to be as much count variability, No? Your CD45 samples range on normalized scale from 2 to 3255. That's 3 orde…
Comment: Ensembl site unresponsive via biomaRt
by
darylruiz6545
• 0
Thank you so much for sharing the link.
Comment: compute_fasta_digest does not match Salmon index hash
by
Alex
• 0
I use the `fastaDigest` tool from [COMBINE-lab/fastaDigest](https://github.com/COMBINE-lab/FastaDigest/), which has the function `compute_f…
Votes
Answer: DESeq: Gene is not flagged as differentially expressed despite count data showin
Two EPIC Methylation Array Analysis Questions
How to get DMR for Infinium methylation EPIC v2
A: GEOquery Fails to Download Series Matrix File
Comment: Gene IDs conversion between Ensembl and NCBI nomenclature for non-model species
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