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Showing :
champ
•
reset
0
votes
8
replies
1.5k
views
Deleted:No significant MVPs with a BH adjusted P-value below 0.05
ChAMP
written 17 months ago by
486342583
• 0
2
votes
10
replies
4.0k
views
Problem at champ.load
ChAMPdata
ChAMP
updated 5 weeks ago by
Josh
• 0 • written 2.0 years ago by
angel
• 0
0
votes
1
reply
461
views
ChAMP.DMR error - Error in makeGenomicRatioSetFromMatrix
ChAMP
updated 4 months ago by
O'Brien
• 0 • written 4 months ago by
André
• 0
0
votes
0
replies
330
views
Errors trying to load EPIC v2 data in ChAMP
ChAMP
ChAMPdata
5 months ago
elgomez
• 0
1
vote
9
replies
3.5k
views
Error using champ.import
ChAMP
EPICv2
updated 6 months ago by
Ricky
• 0 • written 22 months ago by
medha.suman
• 0
1
vote
1
reply
619
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
681
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
4.9k
views
How to get DMR for Infinium methylation EPIC v2
ChAMP
DMRcate
minfi
updated 9 months ago by
Tim Peters
▴ 230 • written 17 months ago by
rae.alshammari
▴ 20
0
votes
1
reply
715
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
498
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
1.6k
views
ChAMP not available for bioconductor 3.19
Bioconductor
ChAMP
updated 11 months ago by
shepherl
4.1k • written 11 months ago by
Macsue
• 0
2
votes
3
replies
915
views
Problem installing ChAMP on a MacBook
ChAMP
updated 11 months ago by
shepherl
4.1k • written 11 months ago by
Galia
• 0
0
votes
7
replies
1.5k
views
ChAMP installation issue
Cha
ChAMP
updated 11 months ago by
James W. MacDonald
68k • written 11 months ago by
e1271094
• 0
2
votes
4
replies
1.2k
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
updated 12 months ago by
James W. MacDonald
68k • written 12 months ago by
Mirella Aurora
• 0
1
vote
2
replies
560
views
Error in champ.load(): The following specified files do not exist
ChAMP
12 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 14 months ago by
James W. MacDonald
68k • written 14 months ago by
david.cheishvili
• 0
0
votes
0
replies
563
views
how to solve this error?
ChAMPdata
ChAMP
14 months ago
Meghana
• 0
0
votes
4
replies
3.0k
views
ChAMP - obtaining beta values using EPICv2 annotation
ChAMP
EPICv2
updated 5 months ago by
icecreamlover
• 0 • written 15 months ago by
ChunkyJones
• 0
0
votes
0
replies
539
views
champ.load() from .idat files of GDC/TCGA dataset
TCGAbiolinks
ChAMP
14 months ago
Thalita
• 0
2
votes
1
reply
1.2k
views
ChAMP can't be found in Bioc3.18?
ChAMP
17 months ago
ramonfallon
▴ 20
0
votes
7
replies
2.5k
views
error with champ.load
ChAMP
champ
methylation
updated 20 months ago by
mike
• 0 • written 5.0 years ago by
jkong
• 0
0
votes
3
replies
1.2k
views
ChAMP trouble reading csv file
ChAMP
written 21 months ago by
Keasiykan
• 0
1
vote
21
replies
5.9k
views
error in ChAMP loading file
ChAMP
updated 14 hours ago by
janwilseo
• 0 • written 2.4 years ago by
Giulia
• 0
3
votes
7
replies
6.7k
views
error with champ.load
champ
written 7.5 years ago by
o.giannakopoulou
▴ 10
0
votes
2
replies
1.7k
views
Trouble Loading Data into Champ
loaddata
ChAMPdata
champload
R
ChAMP
updated 23 months ago by
hfbarrerat
• 0 • written 4.2 years ago by
Bethan
• 0
0
votes
3
replies
1.1k
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
2.0 years ago • updated 24 months ago
arisarkar88
▴ 40
0
votes
1
reply
1.0k
views
Unable to create pd file for ChAMP analysis
ChAMP
updated 10 months ago by
tahirah.yasmin2014
• 0 • written 2.0 years ago by
Monalisa
• 0
0
votes
0
replies
603
views
Cannot generate plots when calling ChAMP
ChAMP
DMP.GUI
2.0 years ago
Kan
• 0
0
votes
2
replies
1.2k
views
error in champ.SVD
svd
methylation
champ
updated 2.0 years ago by
shepherl
4.1k • written 2.0 years 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 2.4 years ago by
James W. MacDonald
68k • written 2.4 years ago by
minardsmitha
▴ 10
1
vote
1
reply
1.0k
views
In readLines(csvfile)
pipeline
testdata
ChAMP
updated 2.4 years ago by
James W. MacDonald
68k • written 2.4 years ago by
luisfranciscoteves
• 0
0
votes
1
reply
892
views
Champ.impute - myLoad not found
ChAMP
updated 2.6 years ago by
Basti
▴ 780 • written 2.6 years ago by
JD
• 0
0
votes
3
replies
1.6k
views
methylated/unmethylated media threshold (EPIC assay)
IlluminaHumanMethylationEPICanno.ilm10b3.hg19
ChAMP
minfi
3.1 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 2.5 years ago by
James W. MacDonald
68k • written 3.0 years ago by
16301050225
• 0
0
votes
4
replies
1.9k
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 3.1 years ago by
Basti
▴ 780 • written 3.1 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
3.5k
views
Error using ChAMP SVD analysis
ChAMP
updated 2.1 years ago by
Seohyun
• 0 • written 3.8 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
3.3 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
3.4 years ago
Paulina
• 0
3
votes
4
replies
11k
views
Problem loading R packages on MacBook Pro
newpackage
ChAMP
updated 2.6 years ago by
Yi Ping
• 0 • written 3.5 years ago by
Brendon
• 0
0
votes
2
replies
1.2k
views
problems opening ChAMP
ChAMP
updated 3.5 years ago by
Basti
▴ 780 • written 3.5 years ago by
AaVee
• 0
0
votes
1
reply
1.4k
views
error in champ.norm
champ.norm
ChAMP
updated 3.6 years ago by
Kevin Blighe
★ 4.0k • written 3.6 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
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Replies
Comment: GSEA preranked analysis downstream of DEseq2
by
Ajay
• 0
`logFC * -log10(pval)` seems to be the pi-score proposed in this [paper][1] [1]: https://pmc.ncbi.nlm.nih.gov/articles/PMC3957066/
Comment: error in ChAMP loading file
by
janwilseo
• 0
Any update on this post? I also had an issue with this. [erosion control](https://charlestonhydroseeding.com/)
Answer: CluserProfiler message "No gene can be mapped"
by
James W. MacDonald
68k
Two things. First, the order of your term2gene is backwards (should be term and then gene, like the name), and by default `enricher` adjust…
Comment: Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis
by
donnycrimson
• 0
One potential workaround might be to adjust for these factors using a combination of design matrices perhaps including batch as a covariate…
Comment: DESeq2 Design controlling for gender
by
donnycrimson
• 0
On a lighter note, while you are tackling such complex data, you might enjoy a quick break playing the [Slope Game](https://slopegame.lol)…
Votes
DiffBind; Error: No sites have activity greater than filter value
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
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