Showing : champ • reset
0
votes
7
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1.3k
views
error with champ.load
ChAMP champ methylation
updated 5 weeks ago by • 0 • written 3.5 years ago by • 0
0
votes
2
replies
185
views
ChAMP trouble reading csv file
ChAMP
updated 9 weeks ago by 63k • written 9 weeks ago by • 0
0
votes
3
replies
368
views
Error using champ.import
ChAMP EPICv2
updated 7 weeks ago by 63k • written 12 weeks ago by • 0
0
votes
18
replies
1.9k
views
error in ChAMP loading file
ChAMP
written 10 months ago by • 0
3
votes
7
replies
4.7k
views
error with champ.load
champ
written 5.9 years ago by ▴ 10
0
votes
2
replies
863
views
Trouble Loading Data into Champ
loaddata ChAMPdata champload R ChAMP
updated 4 months ago by • 0 • written 2.6 years ago by • 0
0
votes
3
replies
382
views
Error in champ.load() function
ChAMP
updated 4 months ago by 63k • written 4 months ago by • 0
0
votes
2
replies
302
views
How to find probe enhancer annotation for Illumina EPIC array?
IlluminaHumanMethylationEPICmanifest ChAMP annotation
updated 4 months ago by 63k • written 4 months ago by • 0
0
votes
2
replies
498
views
Error in loading file using champ.load() from ChAMP package
champ.load epicarray ChAMP methylationArrayAnalysis
5 months ago • updated 4 months ago arisarkar88 ▴ 40
2
votes
3
replies
609
views
Problem at champ.load
ChAMPdata ChAMP
updated 5 months ago by 63k • written 5 months ago by • 0
0
votes
0
replies
254
views
Unable to create pd file for ChAMP analysis
ChAMP
5 months ago Monalisa • 0
0
votes
0
replies
186
views
Cannot generate plots when calling ChAMP
ChAMP DMP.GUI
5 months ago Kan • 0
0
votes
2
replies
381
views
error in champ.SVD
svd methylation champ
updated 5 months ago by 3.5k • written 5 months ago by • 0
0
votes
3
replies
1.0k
views
ChAMP filter bug when using beta matrix and pd as input
ChAMP
written 6.3 years ago by • 0
1
vote
1
reply
367
views
champ.load IDAT files from subdirectories
ChAMP
updated 6 months ago by ▴ 720 • written 6 months ago by • 0
0
votes
1
reply
627
views
Trying to generate a pd file for ChAMP from idat files with no array or slide information in file names
ChAMP
updated 9 months ago by 63k • written 9 months ago by ▴ 10
1
vote
1
reply
385
views
In readLines(csvfile)
pipeline testdata ChAMP
updated 9 months ago by 63k • written 9 months ago by • 0
0
votes
1
reply
305
views
Champ.impute - myLoad not found
ChAMP
updated 12 months ago by ▴ 720 • written 12 months ago by • 0
0
votes
3
replies
899
views
methylated/unmethylated media threshold (EPIC assay)
IlluminaHumanMethylationEPICanno.ilm10b3.hg19 ChAMP minfi
18 months ago • updated 16 months ago ramonfallon • 0
0
votes
1
reply
910
views
champ.SVD() error, assumes standard class() function will return single string
ChAMP
updated 16 months ago by ▴ 720 • written 16 months ago by • 0
0
votes
7
replies
1.9k
views
ERROR happens when install "DSS" package
methylationArrayAnalysis ChAMP DMP DSS
updated 11 months ago by 63k • written 16 months ago by • 0
0
votes
4
replies
957
views
Problem installing ChAMP package.
ChAMP
17 months ago Yu-min • 0
0
votes
1
reply
591
views
How to control for confounders in champ.DMP and champ.DMR?
ChAMP
updated 18 months ago by ▴ 720 • written 18 months ago by • 0
0
votes
1
reply
542
views
Error in ChAMP GUI
ChAMP shiny ChAMPdata
updated 18 months ago by • 0 • written 18 months ago by • 0
1
vote
2
replies
1.9k
views
Error using ChAMP SVD analysis
ChAMP
updated 6 months ago by • 0 • written 2.2 years ago by • 0
0
votes
0
replies
649
views
Error in champ.svd - function 'EstDimRMTv2' within champ.svd acting inconsistently?
minfiData ChAMP
20 months ago behr201 • 0
0
votes
3
replies
794
views
Wrong terminology used on champ.load() output of ChAMP package?
ChAMPdata ChAMP
updated 21 months ago by ▴ 720 • written 21 months ago by • 0
0
votes
0
replies
599
views
Problem loading Red channel idat files with champ.load
R MethylationArrayData ChAMP
22 months ago Paulina • 0
3
votes
4
replies
7.1k
views
Problem loading R packages on MacBook Pro
newpackage ChAMP
updated 12 months ago by • 0 • written 22 months ago by • 0
0
votes
2
replies
623
views
problems opening ChAMP
ChAMP
updated 23 months ago by ▴ 720 • written 23 months ago by • 0
0
votes
1
reply
826
views
error in champ.norm
champ.norm ChAMP
updated 24 months ago by 3.8k • written 24 months ago by • 0
0
votes
0
replies
540
views
ChAMP.CNA analysis
CopyNumberPlots ChAMP CopyNumberVariation CopyNumberVariationData
2.1 years ago FWNL15 • 0
0
votes
2
replies
886
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
2.1 years ago Jinyue • 0
0
votes
5
replies
1.2k
views
Loading ChAMP IdatFiles with two different ArrayTypes
ChAMP
updated 2.2 years ago by ▴ 270 • written 2.2 years ago by • 0
0
votes
6
replies
2.7k
views
Merge problems in R
methylationArrayAnalysis ChAMP MethylationArrayData
2.2 years ago FWNL15 • 0
1
vote
1
reply
969
views
How to solve the error in running champ.DMP()
ChAMP
updated 2.3 years ago by ▴ 720 • written 2.4 years ago by ▴ 10
2
votes
1
reply
799
views
How to save results of each step from ChAMP pipeline?
Bioconductor ChAMP
updated 2.4 years ago by ▴ 270 • written 2.4 years ago by ▴ 10
2
votes
1
reply
869
views
How to download the ChAMP dependency ChAMPdata
ChAMP ChAMPdata
updated 2.4 years ago by 3.5k • written 2.4 years ago by ▴ 10
0
votes
2
replies
1.0k
views
champ.SVD() : Error in while (step == 0) { : missing value where TRUE/FALSE needed
methylationArrayAnalysis EPICarray ChAMP Champ.SVD
2.5 years ago arisarkar88 ▴ 40
0
votes
2
replies
683
views
Error myDMP not found
Illumina methylationArrayAnalysis ChAMPdata ChAMP
2.7 years ago sissialva21 • 0
0
votes
11
replies
5.4k
views
ChAMP input: Beta Matrix?
champ dmr analysis
updated 2.7 years ago by • 0 • written 7.6 years ago by • 0
0
votes
0
replies
457
views
ChAMP batch effect
ChAMP
2.8 years ago SMA180043 • 0
1
vote
2
replies
933
views
what is "sample_well" and "pool_ID" in ChAMP
ChAMP
2.8 years ago Hongbii • 0
2
votes
6
replies
1.9k
views
Blood cell composition adjustment in methylation EPIC array: ChAMP
MethylationArray methylationArrayAnalysis ChAMP
updated 18 months ago by • 0 • written 2.8 years ago by ▴ 20
3
votes
4
replies
1.6k
views
Why the LogFC and delta-beta value are different in ChAMP
DNAMethylation ChAMP
2.8 years ago Hongbii • 0
1
vote
1
reply
592
views
champ.DMP finds different probes in A-vs-B and B-vs-A analysis
DifferentialMethylation ChAMP champ.DMP
updated 2.8 years ago by ▴ 270 • written 2.8 years ago by • 0
1
vote
3
replies
2.1k
views
normalization combination of noob + BMIQ/Quantile
minfi bmiq noob preprocessQuantile champ
updated 3.0 years ago by 63k • written 3.0 years ago by ▴ 50
0
votes
1
reply
598
views
the function DMR in ChAMP package
ChAMP DMR
updated 3.3 years ago by ▴ 270 • written 3.3 years ago by • 0
0
votes
1
reply
506
views
rebuild the ChAMP package
ChAMP
updated 3.5 years ago by 25k • written 3.5 years ago by • 0
0
votes
0
replies
456
views
ChAMP DMP col abbreviations stend for what?
ChAMP
3.5 years ago julie • 0
50 results • Page 1 of 1
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Answer: shinyMethyl - saving the file by Guillaume Devailly ▴ 60
You can probably save individual plots by right-clicking on them an save individual images. Maybe printing the page as a pdf will also work…
Answer: Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq by Michael Love 40k
Did you manually calculate RPMs? Try `fpm(dds)` for comparison, as this also uses DESeq2 median ratio scaling.
Comment: collapseReplicates error after tximeta by Michael Love 40k
A note: I've now changed collapseReplicates() to output a loud warning when it is run on a DESeqDataSet (SummarizedExperiment) with more th…
Comment: Suggested package missing from Development version of Bioconductor by shepherl 3.5k
Have you tried reaching out to the maintainers? If they do not fix the package it will remain unavailable and cause ERROR in your package.…
Answer: Batch effect adjust in model matrix by ATpoint ★ 3.4k
Each sample is a different day, that is called "nested", so there is nothing you can do here. Next time do a better experimental design, he…
Votes
Comment: Batch correction and repeated measures
batch effect : comBat or blocking in limma ?
Batch correction and repeated measures
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
Comment: Phenotype effect - building a contrast matrix - grouping vs interaction
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