Showing : ChAMP • reset
0
votes
2
replies
662
views
Trouble Loading Data into Champ
loaddata ChAMPdata champload R ChAMP
updated 1 day ago by • 0 • written 2.3 years ago by • 0
0
votes
3
replies
172
views
Error in champ.load() function
ChAMP
updated 15 days ago by 63k • written 16 days ago by • 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 63k • written 19 days ago by • 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 63k • written 5 weeks ago by • 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 3.5k • written 6 weeks ago by • 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 • 0
1
vote
1
reply
198
views
champ.load IDAT files from subdirectories
ChAMP
updated 12 weeks ago by ▴ 720 • written 12 weeks ago by • 0
0
votes
12
replies
958
views
error in ChAMP loading file
ChAMP
written 6 months ago by • 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 63k • written 5 months ago by ▴ 10
1
vote
1
reply
248
views
In readLines(csvfile)
pipeline testdata ChAMP
updated 5 months ago by 63k • written 5 months ago by • 0
3
votes
5
replies
4.1k
views
error with champ.load
champ
updated 6 months ago by • 0 • written 5.6 years ago by ▴ 10
0
votes
1
reply
200
views
Champ.impute - myLoad not found
ChAMP
updated 8 months ago by ▴ 720 • written 8 months ago by • 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 ▴ 720 • written 12 months ago by • 0
0
votes
7
replies
1.5k
views
ERROR happens when install "DSS" package
methylationArrayAnalysis ChAMP DMP DSS
updated 7 months ago by 63k • written 12 months ago by • 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 ▴ 720 • written 14 months ago by • 0
0
votes
1
reply
426
views
Error in ChAMP GUI
ChAMP shiny ChAMPdata
updated 14 months ago by • 0 • written 14 months ago by • 0
1
vote
2
replies
1.4k
views
Error using ChAMP SVD analysis
ChAMP
updated 12 weeks ago by • 0 • written 22 months ago by • 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 ▴ 720 • written 17 months ago by • 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 • 0 • written 18 months ago by • 0
0
votes
2
replies
498
views
problems opening ChAMP
ChAMP
updated 19 months ago by ▴ 720 • written 19 months ago by • 0
0
votes
1
reply
640
views
error in champ.norm
champ.norm ChAMP
updated 20 months ago by 3.8k • written 20 months ago by • 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 ▴ 270 • written 22 months ago by • 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 ▴ 720 • written 2.0 years ago by ▴ 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 ▴ 270 • written 2.0 years ago by ▴ 10
2
votes
1
reply
707
views
How to download the ChAMP dependency ChAMPdata
ChAMP ChAMPdata
updated 2.1 years ago by 3.5k • written 2.1 years ago by ▴ 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 • 0 • written 7.2 years ago by • 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 • 0 • written 2.5 years ago by ▴ 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 ▴ 270 • written 2.5 years ago by • 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 63k • written 2.7 years ago by ▴ 50
0
votes
1
reply
494
views
the function DMR in ChAMP package
ChAMP DMR
updated 3.0 years ago by ▴ 270 • written 3.0 years ago by • 0
0
votes
6
replies
978
views
error with champ.load
ChAMP champ methylation
updated 22 months ago by • 0 • written 3.1 years ago by • 0
0
votes
1
reply
389
views
rebuild the ChAMP package
ChAMP
updated 3.2 years ago by 25k • written 3.2 years ago by • 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 ▴ 270 • written 3.3 years ago by • 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
Recent ...
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?
Awards • All
Teacher to James W. MacDonald 63k
Popular Question to Laurent Gatto 1.6k
Popular Question to kevin.rue ▴ 320
Popular Question to Miss Agnieszka Aleksandra Golicz ▴ 40
Popular Question to shepherl 3.5k
Locations • All
United States/Austin Area, 3 minutes ago
United States, 8 minutes ago
WEHI, Melbourne, Australia, 8 minutes ago
Brazil, 36 minutes ago
United States, 52 minutes ago
Traffic: 566 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6