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Showing :
ChAMP
•
reset
0
votes
2
replies
662
views
Trouble Loading Data into Champ
loaddata
ChAMPdata
champload
R
ChAMP
updated 1 day ago by
hfbarrerat
• 0 • written 2.3 years ago by
Bethan
• 0
0
votes
3
replies
172
views
Error in champ.load() function
ChAMP
updated 15 days ago by
James W. MacDonald
63k • written 16 days ago by
Monalisa
• 0
0
votes
2
replies
109
views
How to find probe enhancer annotation for Illumina EPIC array?
IlluminaHumanMethylationEPICmanifest
ChAMP
annotation
updated 19 days ago by
James W. MacDonald
63k • written 19 days ago by
Matilda
• 0
0
votes
2
replies
184
views
Error in loading file using champ.load() from ChAMP package
champ.load
epicarray
ChAMP
methylationArrayAnalysis
5 weeks ago • updated 25 days ago
arisarkar88
▴ 40
2
votes
3
replies
211
views
Problem at champ.load
ChAMPdata
ChAMP
updated 5 weeks ago by
James W. MacDonald
63k • written 5 weeks ago by
angel
• 0
0
votes
0
replies
81
views
Unable to create pd file for ChAMP analysis
ChAMP
6 weeks ago
Monalisa
• 0
0
votes
0
replies
61
views
Cannot generate plots when calling ChAMP
ChAMP
DMP.GUI
6 weeks ago
Kan
• 0
0
votes
2
replies
171
views
error in champ.SVD
svd
methylation
champ
updated 6 weeks ago by
shepherl
3.5k • written 6 weeks ago by
Giulia
• 0
0
votes
3
replies
870
views
ChAMP filter bug when using beta matrix and pd as input
ChAMP
written 5.9 years ago by
allenyuchishing
• 0
1
vote
1
reply
198
views
champ.load IDAT files from subdirectories
ChAMP
updated 12 weeks ago by
Basti
▴ 720 • written 12 weeks ago by
Sin
• 0
0
votes
12
replies
958
views
error in ChAMP loading file
ChAMP
written 6 months ago by
Giulia
• 0
0
votes
1
reply
329
views
Trying to generate a pd file for ChAMP from idat files with no array or slide information in file names
ChAMP
updated 5 months ago by
James W. MacDonald
63k • written 5 months ago by
minardsmitha
▴ 10
1
vote
1
reply
248
views
In readLines(csvfile)
pipeline
testdata
ChAMP
updated 5 months ago by
James W. MacDonald
63k • written 5 months ago by
luisfranciscoteves
• 0
3
votes
5
replies
4.1k
views
error with champ.load
champ
updated 6 months ago by
Roi
• 0 • written 5.6 years ago by
o.giannakopoulou
▴ 10
0
votes
1
reply
200
views
Champ.impute - myLoad not found
ChAMP
updated 8 months ago by
Basti
▴ 720 • written 8 months ago by
JD
• 0
0
votes
3
replies
697
views
methylated/unmethylated media threshold (EPIC assay)
IlluminaHumanMethylationEPICanno.ilm10b3.hg19
ChAMP
minfi
14 months ago • updated 12 months ago
ramonfallon
• 0
0
votes
1
reply
669
views
champ.SVD() error, assumes standard class() function will return single string
ChAMP
updated 12 months ago by
Basti
▴ 720 • written 12 months ago by
ramonfallon
• 0
0
votes
7
replies
1.5k
views
ERROR happens when install "DSS" package
methylationArrayAnalysis
ChAMP
DMP
DSS
updated 7 months ago by
James W. MacDonald
63k • written 12 months ago by
16301050225
• 0
0
votes
4
replies
711
views
Problem installing ChAMP package.
ChAMP
13 months ago
Yu-min
• 0
0
votes
1
reply
466
views
How to control for confounders in champ.DMP and champ.DMR?
ChAMP
updated 14 months ago by
Basti
▴ 720 • written 14 months ago by
l.milicic
• 0
0
votes
1
reply
426
views
Error in ChAMP GUI
ChAMP
shiny
ChAMPdata
updated 14 months ago by
anna.stanislawska
• 0 • written 14 months ago by
Mari
• 0
1
vote
2
replies
1.4k
views
Error using ChAMP SVD analysis
ChAMP
updated 12 weeks ago by
Seohyun
• 0 • written 22 months ago by
FWNL15
• 0
0
votes
0
replies
496
views
Error in champ.svd - function 'EstDimRMTv2' within champ.svd acting inconsistently?
minfiData
ChAMP
16 months ago
behr201
• 0
0
votes
3
replies
664
views
Wrong terminology used on champ.load() output of ChAMP package?
ChAMPdata
ChAMP
updated 17 months ago by
Basti
▴ 720 • written 17 months ago by
mariat
• 0
0
votes
0
replies
496
views
Problem loading Red channel idat files with champ.load
R
MethylationArrayData
ChAMP
18 months ago
Paulina
• 0
3
votes
4
replies
6.3k
views
Problem loading R packages on MacBook Pro
newpackage
ChAMP
updated 8 months ago by
Yi Ping
• 0 • written 18 months ago by
Brendon
• 0
0
votes
2
replies
498
views
problems opening ChAMP
ChAMP
updated 19 months ago by
Basti
▴ 720 • written 19 months ago by
AaVee
• 0
0
votes
1
reply
640
views
error in champ.norm
champ.norm
ChAMP
updated 20 months ago by
Kevin Blighe
3.8k • written 20 months ago by
yu
• 0
0
votes
0
replies
438
views
ChAMP.CNA analysis
CopyNumberPlots
ChAMP
CopyNumberVariation
CopyNumberVariationData
21 months ago
FWNL15
• 0
0
votes
2
replies
716
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
21 months ago
Jinyue
• 0
0
votes
5
replies
870
views
Loading ChAMP IdatFiles with two different ArrayTypes
ChAMP
updated 22 months ago by
Yuan Tian
▴ 270 • written 22 months ago by
FWNL15
• 0
0
votes
6
replies
2.3k
views
Merge problems in R
methylationArrayAnalysis
ChAMP
MethylationArrayData
22 months ago
FWNL15
• 0
1
vote
1
reply
707
views
How to solve the error in running champ.DMP()
ChAMP
updated 2.0 years ago by
Basti
▴ 720 • written 2.0 years ago by
Federica
▴ 10
2
votes
1
reply
640
views
How to save results of each step from ChAMP pipeline?
Bioconductor
ChAMP
updated 2.0 years ago by
Yuan Tian
▴ 270 • written 2.0 years ago by
Federica
▴ 10
2
votes
1
reply
707
views
How to download the ChAMP dependency ChAMPdata
ChAMP
ChAMPdata
updated 2.1 years ago by
shepherl
3.5k • written 2.1 years ago by
Federica
▴ 10
0
votes
2
replies
860
views
champ.SVD() : Error in while (step == 0) { : missing value where TRUE/FALSE needed
methylationArrayAnalysis
EPICarray
ChAMP
Champ.SVD
2.2 years ago • updated 2.1 years ago
arisarkar88
▴ 40
0
votes
2
replies
598
views
Error myDMP not found
Illumina
methylationArrayAnalysis
ChAMPdata
ChAMP
2.3 years ago
sissialva21
• 0
0
votes
11
replies
5.0k
views
ChAMP input: Beta Matrix?
champ
dmr analysis
updated 2.4 years ago by
坤
• 0 • written 7.2 years ago by
Shicheng Guo
• 0
0
votes
0
replies
379
views
ChAMP batch effect
ChAMP
2.5 years ago
SMA180043
• 0
1
vote
2
replies
790
views
what is "sample_well" and "pool_ID" in ChAMP
ChAMP
2.5 years ago
Hongbii
• 0
2
votes
6
replies
1.6k
views
Blood cell composition adjustment in methylation EPIC array: ChAMP
MethylationArray
methylationArrayAnalysis
ChAMP
updated 14 months ago by
l.milicic
• 0 • written 2.5 years ago by
Ankit
▴ 20
3
votes
4
replies
1.4k
views
Why the LogFC and delta-beta value are different in ChAMP
DNAMethylation
ChAMP
2.5 years ago
Hongbii
• 0
1
vote
1
reply
461
views
champ.DMP finds different probes in A-vs-B and B-vs-A analysis
DifferentialMethylation
ChAMP
champ.DMP
updated 2.5 years ago by
Yuan Tian
▴ 270 • written 2.5 years ago by
Ricardo
• 0
1
vote
3
replies
1.8k
views
normalization combination of noob + BMIQ/Quantile
minfi
bmiq
noob
preprocessQuantile
champ
updated 2.7 years ago by
James W. MacDonald
63k • written 2.7 years ago by
Lin
▴ 50
0
votes
1
reply
494
views
the function DMR in ChAMP package
ChAMP
DMR
updated 3.0 years ago by
Yuan Tian
▴ 270 • written 3.0 years ago by
olive8306
• 0
0
votes
6
replies
978
views
error with champ.load
ChAMP
champ
methylation
updated 22 months ago by
Nidhi
• 0 • written 3.1 years ago by
jkong
• 0
0
votes
1
reply
389
views
rebuild the ChAMP package
ChAMP
updated 3.2 years ago by
Martin Morgan
25k • written 3.2 years ago by
olive8306
• 0
0
votes
0
replies
344
views
ChAMP DMP col abbreviations stend for what?
ChAMP
3.2 years ago
julie
• 0
0
votes
1
reply
571
views
about the ChAMP package, the champ.norm output different results,when run it twice on epic data.
ChAMP
updated 3.2 years ago by
Yuan Tian
▴ 270 • written 3.3 years ago by
olive8306
• 0
1
vote
3
replies
914
views
Skewed beta-distribution from Methylation EPIC array data
ChAMP
EPIC
Illumina
Methylation
3.3 years ago
erwin.tomasich
▴ 10
50 results • Page
1 of 1
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Replies
Comment: Question on constructing design matrix and defining contrasts for analysis
by
mohammedtoufiq91
▴ 10
@gordonsmyth thank you, yes, please find the targets frame below. Basically, I want to create a design matrix and binarize by 0 and 1 to be…
Comment: WGCNA: many over and under-expressed features in modules of a signed network
by
andres.firrincieli
▴ 50
answered in Biostars: https://www.biostars.org/p/9564943/
Comment: Multitasking and Rbwa
by
Jean-Philippe Fortin
• 0
Indeed, one can pass additional arguments to the `bwa_aln` function in `Rbwa`: bwa_aln(type="single", index_prefix=index_pr…
Comment: biomaRt error: database disk image is malformed
by
Emile
• 0
UNBORKING the bioMaRt cache `biomaRt::biomartCacheClear()` also fixes the troubles with PANTHER.db installation which have also something t…
Answer: Proteomics data with NA values
by
Laurent Gatto
1.6k
- First, you need to assess how many missing values you have. - I would recommend not to impute your data by 0 (or any arbitrary small …
Votes
Answer: Question on constructing design matrix and defining contrasts for analysis
WGCNA: many over and under-expressed features in modules of a signed network
Comment: WGCNA: many over and under-expressed features in modules of a signed network
Answer: DESeq2 or edgeR for Presence and Absence of Proteins
Answer: Normalized counts from LRT or Wald test?
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