Showing : ChAMP • reset
2
votes
16
replies
2.5k
views
Methylation EPIC array: ChAMP package-champ.load added probes?
methylation epic champ champ.load() Methylation array
updated 4.3 years ago by ▴ 280 • written 4.3 years ago by ▴ 20
1
vote
16
replies
3.3k
views
error in ChAMP loading file
ChAMP
updated 7 weeks ago by • 0 • written 17 months ago by • 0
0
votes
11
replies
6.2k
views
ChAMP input: Beta Matrix?
champ dmr analysis
updated 3.3 years ago by • 0 • written 8.2 years ago by • 0
3
votes
9
replies
3.7k
views
champ.runCombat is failing: "invalid 'row.names' length"
champ
5.7 years ago Gurkenkönig ▴ 10
1
vote
8
replies
2.8k
views
Error in Champ for Bioconductor analyzing Methlayion array data
champ bioconductor contrastmatrix compare.group
updated 5.3 years ago by ▴ 280 • written 5.3 years ago by • 0
0
votes
8
replies
1.4k
views
Error in running the ChAMP test runs from vignette
ChAMP
updated 7.5 years ago by ▴ 90 • written 7.5 years ago by • 0
1
vote
7
replies
1.8k
views
Error using champ.import
ChAMP EPICv2
updated 17 days ago by • 0 • written 10 months ago by • 0
2
votes
7
replies
2.4k
views
Blood cell composition adjustment in methylation EPIC array: ChAMP
MethylationArray methylationArrayAnalysis ChAMP
updated 6 months ago by • 0 • written 3.4 years ago by ▴ 20
3
votes
7
replies
5.4k
views
error with champ.load
champ
written 6.5 years ago by ▴ 10
0
votes
7
replies
631
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
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
7
replies
1.8k
views
error with champ.load
ChAMP champ methylation
updated 8 months ago by • 0 • written 4.1 years ago by • 0
0
votes
6
replies
3.4k
views
Merge problems in R
methylationArrayAnalysis ChAMP MethylationArrayData
2.8 years ago FWNL15 • 0
0
votes
6
replies
1.6k
views
Errors with champ.block
champ champ.block
6.4 years ago tiroshamit • 0
3
votes
6
replies
2.1k
views
could not find function "champ.load"
ChAMP champ 2.9.10 methylationepic
6.1 years ago david.ch • 0
0
votes
6
replies
2.1k
views
ChAMP filter removing good samples from different batch of EPIC arrays.
minfi champ
updated 6.7 years ago by ▴ 90 • written 6.8 years ago by • 0
2
votes
6
replies
1.4k
views
How to get DMR for Infinium methylation EPIC v2
ChAMP DMRcate minfi
updated 4 weeks ago by ▴ 180 • written 5 months ago by ▴ 10
2
votes
5
replies
1.8k
views
Error in Champ for Bioconductor performing GSEA analysis on Methlayion array data
champ bioconductor methyaltion epic array
updated 5.3 years ago by • 0 • written 5.3 years ago by • 0
1
vote
5
replies
2.3k
views
error while using champ.svd() function
champ
5.4 years ago sinha.puja ▴ 10
0
votes
5
replies
2.1k
views
DNA methylation analysis without raw data IDAT files
r illimina 450k methylation minfi champ tcga
updated 5.7 years ago by ▴ 280 • written 5.7 years ago by ▴ 60
2
votes
5
replies
2.3k
views
DMRcate fails in ChAMP package
ChAMP
updated 7.2 years ago by ▴ 90 • written 7.2 years ago by ▴ 10
2
votes
5
replies
1.9k
views
Problem at champ.load
ChAMPdata ChAMP
updated 7 weeks ago by 65k • written 12 months ago by • 0
3
votes
5
replies
2.2k
views
Why the LogFC and delta-beta value are different in ChAMP
DNAMethylation ChAMP
updated 10 weeks ago by • 0 • written 3.4 years ago by • 0
0
votes
5
replies
1.5k
views
Loading ChAMP IdatFiles with two different ArrayTypes
ChAMP
updated 2.8 years ago by ▴ 280 • written 2.8 years ago by • 0
2
votes
4
replies
1.4k
views
bumphunter stalls on "Smoothing coefficients"
bumphunter ChAMP
updated 5.0 years ago by ▴ 280 • written 5.0 years ago by ▴ 10
1
vote
4
replies
2.4k
views
New version of ChAMP can not proceed through champ.DMP
champ
6.7 years ago sarka.vorackova • 0
0
votes
4
replies
1.4k
views
Problem installing ChAMP package.
ChAMP
2.0 years ago Yu-min • 0
0
votes
4
replies
1.1k
views
Taking relatedness among individuals into account in differential methylation analysis?
methylation minfi ChAMP
updated 5.7 years ago by ★ 6.5k • written 5.7 years ago by • 0
1
vote
4
replies
233
views
Error EPICv2 ChAMP
ChAMPdata IlluminaHumanMethylationEPICv2anno.20a1.hg38 ChAMP
updated 12 days ago by 65k • written 16 days ago by • 0
4
votes
4
replies
2.9k
views
How to remove unwanted probes before normalization in 450k data
minfi 450k champ rnbeads
updated 8.1 years ago by 65k • written 8.2 years ago by ▴ 60
3
votes
4
replies
8.6k
views
Problem loading R packages on MacBook Pro
newpackage ChAMP
updated 19 months ago by • 0 • written 2.5 years ago by • 0
3
votes
4
replies
3.0k
views
Error while using champ.svd() function in subset of data
ChAMP methylationepic epicarray epigenomics
updated 6.6 years ago by ▴ 140 • written 6.6 years ago by ▴ 10
1
vote
3
replies
1.5k
views
Error biocLite() newest version of ChAMP
R bioclite champ
6.1 years ago rosa_hegi ▴ 10
0
votes
3
replies
1.5k
views
ChAMP Methylation analysis error code "could not find function champ.load"
champ
5.4 years ago sinha.puja ▴ 10
0
votes
3
replies
720
views
Error in champ.load() function
ChAMP
updated 11 months ago by 65k • written 11 months 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 23 months ago ramonfallon ▴ 20
0
votes
3
replies
1.9k
views
minfi release 1.8
SNP Annotation GO probe SNPlocs PROcess minfi bumphunter ChAMP SNP Annotation GO probe
updated 10.2 years ago by ▴ 20 • written 10.3 years ago by ★ 4.2k
0
votes
3
replies
1.2k
views
Error when running ChAMP package
champ
5.9 years ago hazel.rogers • 0
0
votes
3
replies
661
views
ChAMP trouble reading csv file
ChAMP
written 9 months ago by • 0
0
votes
3
replies
1.9k
views
error in champ.DMR using DMRcate (v2.8.3)
champ dmrcate IlluminaHumanMethylationEPICanno.ilm10b2.hg19
updated 6.9 years ago by ▴ 90 • written 6.9 years ago by • 0
0
votes
3
replies
1.3k
views
ChAMP filter bug when using beta matrix and pd as input
ChAMP
written 6.9 years ago by • 0
2
votes
3
replies
2.2k
views
Error in champ.load (v. 2.8.3)
champ ChAMP
updated 6.9 years ago by ▴ 90 • written 6.9 years ago by ▴ 10
0
votes
3
replies
1.2k
views
missing value in beta matrix after normalization wich champ.norm
champ champs.svd() champ.norm
6.2 years ago jfertaj ▴ 30
2
votes
3
replies
1.6k
views
champ.impute doesn't update beta matrix
champ impute bioconductor
updated 7.1 years ago by ▴ 90 • written 7.1 years ago by ▴ 10
0
votes
3
replies
7.6k
views
Downgrading R to an older version
MEDIPS ChAMP MEDIPS ChAMP
updated 9.7 years ago by ★ 8.2k • written 9.7 years ago by ▴ 70
2
votes
3
replies
1.7k
views
ChAMP was installed and library in R, however, I can't use the function
champ
6.1 years ago doctorjiangtao ▴ 10
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
3
replies
1.4k
views
QC and normalization of 450K data from CSVs instead of IDATs
450K CSV normalization minfi ChAMP
updated 5.9 years ago by ▴ 280 • written 5.9 years ago by ▴ 190
1
vote
3
replies
2.2k
views
champ.DMP phenotypes and covariates
champ champ.dmp()
updated 6.5 years ago by ▴ 280 • written 6.5 years ago by ▴ 10
1
vote
3
replies
2.7k
views
normalization combination of noob + BMIQ/Quantile
minfi bmiq noob preprocessQuantile champ
updated 3.6 years ago by 65k • written 3.6 years ago by ▴ 50
50 results • Page 1 of 1
Recent ...
Replies
Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19 (as at 4 May 2024). In the meantime, you could consider using the goana() and kegga() …
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
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