Showing : champ • reset
1
vote
18
replies
7.4k
views
error in ChAMP loading file
ChAMP
updated 5 months ago by • 0 • written 3.1 years ago by • 0
0
votes
8
replies
1.8k
views
Deleted:No significant MVPs with a BH adjusted P-value below 0.05
ChAMP
written 2.0 years ago by • 0
2
votes
10
replies
4.5k
views
Problem at champ.load
ChAMPdata ChAMP
updated 8 months ago by • 0 • written 2.6 years ago by • 0
0
votes
1
reply
655
views
ChAMP.DMR error - Error in makeGenomicRatioSetFromMatrix
ChAMP
updated 11 months ago by • 0 • written 11 months ago by • 0
0
votes
0
replies
570
views
Errors trying to load EPIC v2 data in ChAMP
ChAMP ChAMPdata
13 months ago elgomez • 0
1
vote
9
replies
3.8k
views
Error using champ.import
ChAMP EPICv2
updated 13 months ago by • 0 • written 2.4 years ago by • 0
1
vote
1
reply
810
views
Empty Results from champ.DMP Despite Expected Output
MethylationArray ChAMP R
updated 15 months ago by 68k • written 15 months ago by • 0
0
votes
4
replies
986
views
Failed to install geneLenDataBase
geneLenDataBase ChAMP
updated 16 months ago by 4.2k • written 16 months ago by • 0
4
votes
12
replies
5.8k
views
How to get DMR for Infinium methylation EPIC v2
ChAMP DMRcate minfi
updated 16 months ago by ▴ 230 • written 2.0 years ago by ▴ 20
0
votes
1
reply
939
views
ChAMP analysis Error: Meth Matrix and UnMeth Matrix seems not paried correctly AND incomplete final line
MethylationArray methylationArrayAnalysis ChAMP
updated 12 months ago by • 0 • written 17 months ago by • 0
0
votes
1
reply
697
views
single excel file containing methylation beta values does not get loaded in ChAMP
ChAMP
updated 17 months ago by ▴ 780 • written 17 months ago by • 0
0
votes
3
replies
1.9k
views
ChAMP not available for bioconductor 3.19
Bioconductor ChAMP
updated 18 months ago by 4.2k • written 18 months ago by • 0
2
votes
3
replies
1.1k
views
Problem installing ChAMP on a MacBook
ChAMP
updated 19 months ago by 4.2k • written 19 months ago by • 0
0
votes
7
replies
2.1k
views
ChAMP installation issue
Cha ChAMP
updated 18 months ago by 68k • written 19 months ago by • 0
2
votes
4
replies
1.6k
views
Error EPICv2 ChAMP
ChAMPdata IlluminaHumanMethylationEPICv2anno.20a1.hg38 ChAMP
updated 19 months ago by 68k • written 19 months ago by • 0
1
vote
2
replies
741
views
Error in champ.load(): The following specified files do not exist
ChAMP
19 months ago Sherin • 0
1
vote
1
reply
1.7k
views
Need Advice: Issue with ChAMP Analysis - Meth and UnMeth Matrix Pairing Error
MethylationArray methylationArrayAnalysis ChAMP
updated 21 months ago by 68k • written 21 months ago by • 0
0
votes
0
replies
717
views
how to solve this error?
ChAMPdata ChAMP
21 months ago Meghana • 0
0
votes
4
replies
3.6k
views
ChAMP - obtaining beta values using EPICv2 annotation
ChAMP EPICv2
updated 13 months ago by • 0 • written 23 months ago by • 0
0
votes
0
replies
671
views
champ.load() from .idat files of GDC/TCGA dataset
TCGAbiolinks ChAMP
22 months ago Thalita • 0
2
votes
1
reply
1.4k
views
ChAMP can't be found in Bioc3.18?
ChAMP
2.1 years ago ramonfallon ▴ 20
0
votes
7
replies
2.8k
views
error with champ.load
ChAMP champ methylation
updated 2.3 years ago by • 0 • written 5.7 years ago by • 0
0
votes
3
replies
1.3k
views
ChAMP trouble reading csv file
ChAMP
written 2.4 years ago by • 0
3
votes
7
replies
7.0k
views
error with champ.load
champ
written 8.1 years ago by ▴ 10
0
votes
2
replies
1.9k
views
Trouble Loading Data into Champ
loaddata ChAMPdata champload R ChAMP
updated 2.5 years ago by • 0 • written 4.8 years ago by • 0
0
votes
3
replies
1.2k
views
Error in champ.load() function
ChAMP
updated 2.6 years ago by 68k • written 2.6 years ago by • 0
0
votes
2
replies
1.7k
views
How to find probe enhancer annotation for Illumina EPIC array?
IlluminaHumanMethylationEPICmanifest ChAMP annotation
updated 2.6 years ago by 68k • written 2.6 years ago by • 0
0
votes
2
replies
1.8k
views
Error in loading file using champ.load() from ChAMP package
champ.load epicarray ChAMP methylationArrayAnalysis
2.6 years ago arisarkar88 ▴ 40
0
votes
1
reply
1.2k
views
Unable to create pd file for ChAMP analysis
ChAMP
updated 17 months ago by • 0 • written 2.6 years ago by • 0
0
votes
0
replies
716
views
Cannot generate plots when calling ChAMP
ChAMP DMP.GUI
2.6 years ago Kan • 0
0
votes
2
replies
1.3k
views
error in champ.SVD
svd methylation champ
updated 2.7 years ago by 4.2k • written 2.7 years ago by • 0
0
votes
3
replies
1.9k
views
ChAMP filter bug when using beta matrix and pd as input
ChAMP
written 8.5 years ago by • 0
1
vote
1
reply
1.5k
views
champ.load IDAT files from subdirectories
ChAMP
updated 2.8 years ago by ▴ 780 • written 2.8 years ago by • 0
0
votes
1
reply
2.1k
views
Trying to generate a pd file for ChAMP from idat files with no array or slide information in file names
ChAMP
updated 3.0 years ago by 68k • written 3.0 years ago by ▴ 10
1
vote
1
reply
1.2k
views
In readLines(csvfile)
pipeline testdata ChAMP
updated 3.0 years ago by 68k • written 3.0 years ago by • 0
0
votes
1
reply
1.0k
views
Champ.impute - myLoad not found
ChAMP
updated 3.2 years ago by ▴ 780 • written 3.2 years ago by • 0
0
votes
3
replies
1.8k
views
methylated/unmethylated media threshold (EPIC assay)
IlluminaHumanMethylationEPICanno.ilm10b3.hg19 ChAMP minfi
3.7 years ago • updated 3.6 years ago ramonfallon ▴ 20
0
votes
1
reply
1.8k
views
champ.SVD() error, assumes standard class() function will return single string
ChAMP
updated 3.6 years ago by ▴ 780 • written 3.6 years ago by ▴ 20
0
votes
7
replies
3.8k
views
ERROR happens when install "DSS" package
methylationArrayAnalysis ChAMP DMP DSS
updated 3.1 years ago by 68k • written 3.6 years ago by • 0
0
votes
4
replies
2.1k
views
Problem installing ChAMP package.
ChAMP
3.6 years ago Yu-min • 0
0
votes
1
reply
1.5k
views
How to control for confounders in champ.DMP and champ.DMR?
ChAMP
updated 3.7 years ago by ▴ 780 • written 3.7 years ago by • 0
0
votes
1
reply
1.3k
views
Error in ChAMP GUI
ChAMP shiny ChAMPdata
updated 3.7 years ago by • 0 • written 3.7 years ago by • 0
1
vote
2
replies
3.8k
views
Error using ChAMP SVD analysis
ChAMP
updated 2.8 years ago by • 0 • written 4.4 years ago by • 0
0
votes
0
replies
1.3k
views
Error in champ.svd - function 'EstDimRMTv2' within champ.svd acting inconsistently?
minfiData ChAMP
3.9 years ago behr201 • 0
0
votes
3
replies
1.6k
views
Wrong terminology used on champ.load() output of ChAMP package?
ChAMPdata ChAMP
updated 4.0 years ago by ▴ 780 • written 4.0 years ago by • 0
0
votes
0
replies
1.3k
views
Problem loading Red channel idat files with champ.load
R MethylationArrayData ChAMP
4.0 years ago Paulina • 0
3
votes
4
replies
12k
views
Problem loading R packages on MacBook Pro
newpackage ChAMP
updated 3.2 years ago by • 0 • written 4.1 years ago by • 0
0
votes
2
replies
1.3k
views
problems opening ChAMP
ChAMP
updated 4.1 years ago by ▴ 780 • written 4.1 years ago by • 0
0
votes
1
reply
1.6k
views
error in champ.norm
champ.norm ChAMP
updated 4.2 years ago by ★ 4.0k • written 4.2 years ago by • 0
0
votes
0
replies
1.2k
views
ChAMP.CNA analysis
CopyNumberPlots ChAMP CopyNumberVariation CopyNumberVariationData
4.3 years ago FWNL15 • 0
156 results • Page 1 of 4
Recent ...
Replies
Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Awards • All
Popular Question to James W. MacDonald 68k
Popular Question to Gordon Smyth 53k
Commentator to sina.nassiri ▴ 130
Popular Question to Hervé Pagès 16k
Popular Question to jared.andrews07 ▴ 30
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