Showing : ChAMP • reset
1
vote
4
replies
249
views
Error EPICv2 ChAMP
ChAMPdata IlluminaHumanMethylationEPICv2anno.20a1.hg38 ChAMP
updated 17 days ago by 65k • written 21 days ago by • 0
1
vote
2
replies
165
views
Error in champ.load(): The following specified files do not exist
ChAMP
22 days ago • updated 21 days ago Sherin • 0
1
vote
1
reply
308
views
Need Advice: Issue with ChAMP Analysis - Meth and UnMeth Matrix Pairing Error
MethylationArray methylationArrayAnalysis ChAMP
updated 11 weeks ago by 65k • written 11 weeks ago by • 0
0
votes
0
replies
221
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how to solve this error?
ChAMPdata ChAMP
11 weeks ago Meghana • 0
0
votes
0
replies
161
views
champ.load() from .idat files of GDC/TCGA dataset
TCGAbiolinks ChAMP
3 months ago Thalita • 0
0
votes
2
replies
692
views
ChAMP - obtaining beta values using EPICv2 annotation
ChAMP EPICv2
updated 3 months ago by • 0 • written 4 months ago by • 0
0
votes
7
replies
652
views
Deleted:No significant MVPs with a BH adjusted P-value below 0.05
ChAMP
updated 5 months ago by ▴ 780 • written 5 months ago by • 0
2
votes
6
replies
1.4k
views
How to get DMR for Infinium methylation EPIC v2
ChAMP DMRcate minfi
updated 5 weeks ago by ▴ 180 • written 5 months ago by ▴ 10
2
votes
1
reply
598
views
ChAMP can't be found in Bioc3.18?
ChAMP
5 months ago ramonfallon ▴ 20
0
votes
3
replies
673
views
ChAMP trouble reading csv file
ChAMP
written 9 months ago by • 0
1
vote
7
replies
1.8k
views
Error using champ.import
ChAMP EPICv2
updated 22 days ago by • 0 • written 10 months ago by • 0
0
votes
3
replies
728
views
Error in champ.load() function
ChAMP
updated 11 months ago by 65k • written 12 months ago by • 0
0
votes
2
replies
719
views
How to find probe enhancer annotation for Illumina EPIC array?
IlluminaHumanMethylationEPICmanifest ChAMP annotation
updated 12 months ago by 65k • written 12 months ago by • 0
0
votes
2
replies
1.0k
views
Error in loading file using champ.load() from ChAMP package
champ.load epicarray ChAMP methylationArrayAnalysis
12 months ago arisarkar88 ▴ 40
2
votes
5
replies
1.9k
views
Problem at champ.load
ChAMPdata ChAMP
updated 8 weeks ago by 65k • written 12 months ago by • 0
0
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0
replies
592
views
Unable to create pd file for ChAMP analysis
ChAMP
12 months ago Monalisa • 0
0
votes
0
replies
394
views
Cannot generate plots when calling ChAMP
ChAMP DMP.GUI
12 months ago Kan • 0
0
votes
2
replies
758
views
error in champ.SVD
svd methylation champ
updated 13 months ago by 3.9k • written 13 months ago by • 0
1
vote
1
reply
766
views
champ.load IDAT files from subdirectories
ChAMP
updated 14 months ago by ▴ 780 • written 14 months ago by • 0
0
votes
1
reply
1.2k
views
Trying to generate a pd file for ChAMP from idat files with no array or slide information in file names
ChAMP
updated 17 months ago by 65k • written 17 months ago by ▴ 10
1
vote
1
reply
670
views
In readLines(csvfile)
pipeline testdata ChAMP
updated 17 months ago by 65k • written 17 months ago by • 0
1
vote
16
replies
3.3k
views
error in ChAMP loading file
ChAMP
updated 8 weeks ago by • 0 • written 17 months ago by • 0
0
votes
1
reply
561
views
Champ.impute - myLoad not found
ChAMP
updated 19 months ago by ▴ 780 • written 19 months ago by • 0
0
votes
1
reply
1.2k
views
champ.SVD() error, assumes standard class() function will return single string
ChAMP
updated 24 months ago by ▴ 780 • written 24 months ago by ▴ 20
0
votes
7
replies
2.6k
views
ERROR happens when install "DSS" package
methylationArrayAnalysis ChAMP DMP DSS
updated 18 months ago by 65k • written 24 months ago by • 0
0
votes
4
replies
1.4k
views
Problem installing ChAMP package.
ChAMP
2.1 years ago Yu-min • 0
0
votes
1
reply
874
views
How to control for confounders in champ.DMP and champ.DMR?
ChAMP
updated 2.1 years ago by ▴ 780 • written 2.1 years ago by • 0
0
votes
3
replies
1.2k
views
methylated/unmethylated media threshold (EPIC assay)
IlluminaHumanMethylationEPICanno.ilm10b3.hg19 ChAMP minfi
2.1 years ago • updated 24 months ago ramonfallon ▴ 20
0
votes
1
reply
803
views
Error in ChAMP GUI
ChAMP shiny ChAMPdata
updated 2.1 years ago by • 0 • written 2.2 years ago by • 0
0
votes
0
replies
875
views
Error in champ.svd - function 'EstDimRMTv2' within champ.svd acting inconsistently?
minfiData ChAMP
2.3 years ago behr201 • 0
0
votes
3
replies
1.1k
views
Wrong terminology used on champ.load() output of ChAMP package?
ChAMPdata ChAMP
updated 2.4 years ago by ▴ 780 • written 2.4 years ago by • 0
0
votes
0
replies
838
views
Problem loading Red channel idat files with champ.load
R MethylationArrayData ChAMP
2.4 years ago Paulina • 0
3
votes
4
replies
8.7k
views
Problem loading R packages on MacBook Pro
newpackage ChAMP
updated 19 months ago by • 0 • written 2.5 years ago by • 0
0
votes
2
replies
856
views
problems opening ChAMP
ChAMP
updated 2.5 years ago by ▴ 780 • written 2.5 years ago by • 0
0
votes
1
reply
1.1k
views
error in champ.norm
champ.norm ChAMP
updated 2.6 years ago by ★ 3.9k • written 2.6 years ago by • 0
0
votes
0
replies
764
views
ChAMP.CNA analysis
CopyNumberPlots ChAMP CopyNumberVariation CopyNumberVariationData
2.7 years ago FWNL15 • 0
0
votes
2
replies
1.2k
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
2.7 years ago Jinyue • 0
0
votes
5
replies
1.6k
views
Loading ChAMP IdatFiles with two different ArrayTypes
ChAMP
updated 2.8 years ago by ▴ 280 • written 2.8 years ago by • 0
0
votes
6
replies
3.4k
views
Merge problems in R
methylationArrayAnalysis ChAMP MethylationArrayData
2.8 years ago FWNL15 • 0
1
vote
2
replies
2.6k
views
Error using ChAMP SVD analysis
ChAMP
updated 14 months ago by • 0 • written 2.8 years ago by • 0
1
vote
1
reply
1.3k
views
How to solve the error in running champ.DMP()
ChAMP
updated 3.0 years ago by ▴ 780 • written 3.0 years ago by ▴ 10
2
votes
1
reply
1.0k
views
How to save results of each step from ChAMP pipeline?
Bioconductor ChAMP
updated 3.0 years ago by ▴ 280 • written 3.0 years ago by ▴ 10
2
votes
1
reply
1.3k
views
How to download the ChAMP dependency ChAMPdata
ChAMP ChAMPdata
updated 3.0 years ago by 3.9k • written 3.0 years ago by ▴ 10
0
votes
2
replies
1.4k
views
champ.SVD() : Error in while (step == 0) { : missing value where TRUE/FALSE needed
methylationArrayAnalysis EPICarray ChAMP Champ.SVD
3.1 years ago arisarkar88 ▴ 40
0
votes
2
replies
1.2k
views
Trouble Loading Data into Champ
loaddata ChAMPdata champload R ChAMP
updated 11 months ago by • 0 • written 3.2 years ago by • 0
0
votes
2
replies
877
views
Error myDMP not found
Illumina methylationArrayAnalysis ChAMPdata ChAMP
3.3 years ago sissialva21 • 0
0
votes
0
replies
608
views
ChAMP batch effect
ChAMP
3.4 years ago SMA180043 • 0
1
vote
2
replies
1.1k
views
what is "sample_well" and "pool_ID" in ChAMP
ChAMP
3.4 years ago Hongbii • 0
3
votes
5
replies
2.2k
views
Why the LogFC and delta-beta value are different in ChAMP
DNAMethylation ChAMP
updated 11 weeks ago by • 0 • written 3.4 years ago by • 0
2
votes
7
replies
2.4k
views
Blood cell composition adjustment in methylation EPIC array: ChAMP
MethylationArray methylationArrayAnalysis ChAMP
updated 7 months ago by • 0 • written 3.4 years ago by ▴ 20
50 results • Page 1 of 1
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Comment: How to use spike-in information (sequences from another species) with DESeq2::DE by maria.soler • 0
Hi, I have a question barely related to this topic. Do you use a custom reference genome combining your organism and the one used as a spik…
Answer: Differential gene expression analysis results by ATpoint ★ 4.1k
Pease do not open multiple posts for the same issue: https://support.bioconductor.org/p/9158194/#9158222 The support site is not meant f…
Comment: deseq2 results by sajadahmad41454 • 0
thank you for your response, should i remove or discard that sample? since the red outlier on left represents one of healthy samples.
Comment: deseq2 results by swbarnes2 ★ 1.4k
It looks like the PCA plot of a real RNASeq experiment. The red outlier on the left might be the mathematical reason why you have few vali…
Comment: Multi-factorial, longitudinal disease progression analysis with unbalanced patie by Dylan.Sheerin • 0
Thank you very much, Gordon. I'll give voomLmFit a go!
Votes
Comment: deseq2 results
Comment: deseq2 results
Answer: Multi-factorial, longitudinal disease progression analysis with unbalanced patie
Answer: Extremely small p-values using Limma for proteomic data
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