Showing : champ • reset
0
votes
1
reply
337
views
ChAMP.DMR error - Error in makeGenomicRatioSetFromMatrix
ChAMP
updated 4 weeks ago by • 0 • written 5 weeks ago by • 0
0
votes
0
replies
203
views
Errors trying to load EPIC v2 data in ChAMP
ChAMP ChAMPdata
11 weeks ago elgomez • 0
1
vote
9
replies
3.1k
views
Error using champ.import
ChAMP EPICv2
updated 3 months ago by • 0 • written 19 months ago by • 0
1
vote
1
reply
456
views
Empty Results from champ.DMP Despite Expected Output
MethylationArray ChAMP R
updated 4 months ago by 67k • written 4 months ago by • 0
0
votes
4
replies
573
views
Failed to install geneLenDataBase
geneLenDataBase ChAMP
updated 5 months ago by 4.1k • written 5 months ago by • 0
3
votes
12
replies
4.0k
views
How to get DMR for Infinium methylation EPIC v2
ChAMP DMRcate minfi
updated 6 months ago by ▴ 200 • written 14 months ago by ▴ 10
0
votes
1
reply
548
views
ChAMP analysis Error: Meth Matrix and UnMeth Matrix seems not paried correctly AND incomplete final line
MethylationArray methylationArrayAnalysis ChAMP
updated 8 weeks ago by • 0 • written 6 months ago by • 0
0
votes
1
reply
405
views
single excel file containing methylation beta values does not get loaded in ChAMP
ChAMP
updated 7 months ago by ▴ 780 • written 7 months ago by • 0
0
votes
3
replies
1.3k
views
ChAMP not available for bioconductor 3.19
Bioconductor ChAMP
updated 8 months ago by 4.1k • written 8 months ago by • 0
2
votes
3
replies
782
views
Problem installing ChAMP on a MacBook
ChAMP
updated 8 months ago by 4.1k • written 8 months ago by • 0
0
votes
7
replies
1.3k
views
ChAMP installation issue
Cha ChAMP
updated 8 months ago by 67k • written 8 months ago by • 0
2
votes
4
replies
981
views
Error EPICv2 ChAMP
ChAMPdata IlluminaHumanMethylationEPICv2anno.20a1.hg38 ChAMP
updated 9 months ago by 67k • written 9 months ago by • 0
1
vote
2
replies
474
views
Error in champ.load(): The following specified files do not exist
ChAMP
9 months ago Sherin • 0
1
vote
1
reply
1.2k
views
Need Advice: Issue with ChAMP Analysis - Meth and UnMeth Matrix Pairing Error
MethylationArray methylationArrayAnalysis ChAMP
updated 11 months ago by 67k • written 11 months ago by • 0
0
votes
0
replies
479
views
how to solve this error?
ChAMPdata ChAMP
11 months ago Meghana • 0
0
votes
4
replies
2.4k
views
ChAMP - obtaining beta values using EPICv2 annotation
ChAMP EPICv2
updated 11 weeks ago by • 0 • written 12 months ago by • 0
0
votes
0
replies
475
views
champ.load() from .idat files of GDC/TCGA dataset
TCGAbiolinks ChAMP
12 months ago Thalita • 0
0
votes
7
replies
1.2k
views
Deleted:No significant MVPs with a BH adjusted P-value below 0.05
ChAMP
updated 14 months ago by ▴ 780 • written 14 months ago by • 0
2
votes
1
reply
1.1k
views
ChAMP can't be found in Bioc3.18?
ChAMP
14 months ago ramonfallon ▴ 20
0
votes
7
replies
2.3k
views
error with champ.load
ChAMP champ methylation
updated 17 months ago by • 0 • written 4.8 years ago by • 0
0
votes
3
replies
1.1k
views
ChAMP trouble reading csv file
ChAMP
written 18 months ago by • 0
1
vote
16
replies
4.6k
views
error in ChAMP loading file
ChAMP
updated 10 months ago by • 0 • written 2.2 years ago by • 0
3
votes
7
replies
6.4k
views
error with champ.load
champ
written 7.2 years ago by ▴ 10
0
votes
2
replies
1.6k
views
Trouble Loading Data into Champ
loaddata ChAMPdata champload R ChAMP
updated 20 months ago by • 0 • written 3.9 years ago by • 0
0
votes
3
replies
986
views
Error in champ.load() function
ChAMP
updated 20 months ago by 67k • written 20 months ago by • 0
0
votes
2
replies
1.3k
views
How to find probe enhancer annotation for Illumina EPIC array?
IlluminaHumanMethylationEPICmanifest ChAMP annotation
updated 20 months ago by 67k • written 20 months ago by • 0
0
votes
2
replies
1.5k
views
Error in loading file using champ.load() from ChAMP package
champ.load epicarray ChAMP methylationArrayAnalysis
21 months ago arisarkar88 ▴ 40
2
votes
8
replies
3.3k
views
Problem at champ.load
ChAMPdata ChAMP
updated 11 weeks ago by • 0 • written 21 months ago by • 0
0
votes
1
reply
924
views
Unable to create pd file for ChAMP analysis
ChAMP
updated 7 months ago by • 0 • written 21 months ago by • 0
0
votes
0
replies
552
views
Cannot generate plots when calling ChAMP
ChAMP DMP.GUI
21 months ago Kan • 0
0
votes
2
replies
1.1k
views
error in champ.SVD
svd methylation champ
updated 21 months ago by 4.1k • written 21 months ago by • 0
0
votes
3
replies
1.6k
views
ChAMP filter bug when using beta matrix and pd as input
ChAMP
written 7.6 years ago by • 0
1
vote
1
reply
1.1k
views
champ.load IDAT files from subdirectories
ChAMP
updated 23 months ago by ▴ 780 • written 23 months ago by • 0
0
votes
1
reply
1.7k
views
Trying to generate a pd file for ChAMP from idat files with no array or slide information in file names
ChAMP
updated 2.1 years ago by 67k • written 2.1 years ago by ▴ 10
1
vote
1
reply
931
views
In readLines(csvfile)
pipeline testdata ChAMP
updated 2.1 years ago by 67k • written 2.1 years ago by • 0
0
votes
1
reply
808
views
Champ.impute - myLoad not found
ChAMP
updated 2.3 years ago by ▴ 780 • written 2.3 years ago by • 0
0
votes
3
replies
1.5k
views
methylated/unmethylated media threshold (EPIC assay)
IlluminaHumanMethylationEPICanno.ilm10b3.hg19 ChAMP minfi
2.8 years ago • updated 2.7 years ago ramonfallon ▴ 20
0
votes
1
reply
1.5k
views
champ.SVD() error, assumes standard class() function will return single string
ChAMP
updated 2.7 years ago by ▴ 780 • written 2.7 years ago by ▴ 20
0
votes
7
replies
3.3k
views
ERROR happens when install "DSS" package
methylationArrayAnalysis ChAMP DMP DSS
updated 2.3 years ago by 67k • written 2.7 years ago by • 0
0
votes
4
replies
1.8k
views
Problem installing ChAMP package.
ChAMP
2.8 years ago Yu-min • 0
0
votes
1
reply
1.2k
views
How to control for confounders in champ.DMP and champ.DMR?
ChAMP
updated 2.8 years ago by ▴ 780 • written 2.8 years ago by • 0
0
votes
1
reply
1.1k
views
Error in ChAMP GUI
ChAMP shiny ChAMPdata
updated 2.9 years ago by • 0 • written 2.9 years ago by • 0
1
vote
2
replies
3.3k
views
Error using ChAMP SVD analysis
ChAMP
updated 23 months ago by • 0 • written 3.5 years ago by • 0
0
votes
0
replies
1.1k
views
Error in champ.svd - function 'EstDimRMTv2' within champ.svd acting inconsistently?
minfiData ChAMP
3.1 years ago behr201 • 0
0
votes
3
replies
1.3k
views
Wrong terminology used on champ.load() output of ChAMP package?
ChAMPdata ChAMP
updated 3.1 years ago by ▴ 780 • written 3.1 years ago by • 0
0
votes
0
replies
1.1k
views
Problem loading Red channel idat files with champ.load
R MethylationArrayData ChAMP
3.2 years ago Paulina • 0
3
votes
4
replies
10k
views
Problem loading R packages on MacBook Pro
newpackage ChAMP
updated 2.4 years ago by • 0 • written 3.2 years ago by • 0
0
votes
2
replies
1.1k
views
problems opening ChAMP
ChAMP
updated 3.3 years ago by ▴ 780 • written 3.3 years ago by • 0
0
votes
1
reply
1.4k
views
error in champ.norm
champ.norm ChAMP
updated 3.3 years ago by ★ 4.0k • written 3.3 years ago by • 0
0
votes
0
replies
960
views
ChAMP.CNA analysis
CopyNumberPlots ChAMP CopyNumberVariation CopyNumberVariationData
3.4 years ago FWNL15 • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: How to visualize these pathways using pathview by Guido Hooiveld ★ 4.1k
FYI: a similar, if not identical issue has been reported before (`pathview` has problems visualizing some pathways, but not all). You likel…
Comment: Why select top highly expressed genes based on normalized counts, but then plot by Quang NN ▴ 10
I see. Thank you ATpoint!
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by Prakash Sah • 0
Thanks James!
Comment: Why select top highly expressed genes based on normalized counts, but then plot by ATpoint ★ 4.6k
I think I explained what the differences between approach 1 and 2 is in my answer. I assume that the tutorial uses vst because it is varian…
Comment: Why select top highly expressed genes based on normalized counts, but then plot by Quang NN ▴ 10
Thank you ATpoint for your responses. I am a bit confused because the difference between the two approaches is the selection of the genes…
Votes
Comment: can't install tscR
Answer: Csaw normalization strategies - general inquiry
A: DESeq2 interaction term
Comment: Recount3 data correspond to TCGA data
Answer: DESeq2- merging technical vs biological replicates
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