Showing : DMRcate • reset
1
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2
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308
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limma Intercept vs No-intercept models completely changing DMR results?
limma DMRcate MethylationArray EPICV2
updated 1 day ago by 50k • written 1 day ago by • 0
1
vote
2
replies
992
views
DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE, : NA/NaN/Inf in foreign function call (arg 1)"
DMRcate Gviz
updated 12 days ago by ▴ 180 • written 14 months ago by ▴ 10
0
votes
0
replies
91
views
DMRcate error need at least two non-NA values to interpolate
DNAMethylation DMRcate
4 weeks ago Macsue • 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
0
votes
2
replies
527
views
EPIC array hg38 annotation?
minfi DMRcate
12 weeks ago • updated 11 weeks ago mycetes • 0
0
votes
0
replies
132
views
What is the significance of DMR in DMRcate
DMRcate
3 months ago chuanjiao6 • 0
3
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2
replies
275
views
Question about DMRcate
DMRcate dmrcate
3 months ago chuanjiao6 • 0
8
votes
7
replies
1.2k
views
Why is DMRcate not available for Bioconductor version 3.18?
DMRcate
written 5 months ago by ▴ 30
0
votes
5
replies
606
views
error while running DMRcate
stattistics epicarray Epigenetics DMRcate
updated 6 months ago by 65k • written 6 months ago by ▴ 10
0
votes
1
reply
750
views
DMR.plot() Error in .local(.Object, ...) : Failed to obtain 'hguid' cookie
DMRcate DMR.plot
updated 6 months ago by 3.9k • written 6 months ago by • 0
3
votes
4
replies
865
views
DMRcate design
Epigenetics EpigeneticsWorkflow DMRcate
7 months ago Jitendra ▴ 10
0
votes
1
reply
482
views
dmrcate needs at least two non-NA values to interpolate
miss DMRcate missMethyl
updated 8 months ago by ▴ 180 • written 8 months ago by • 0
2
votes
6
replies
1.1k
views
cpg.annotate() in DMRcate error
DNAMethylation methylationArrayAnalysis DMRcate MethylationArrayData MethylationArray
updated 12 months ago by ▴ 180 • written 12 months ago by • 0
6
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12
replies
1.8k
views
Error when loading DMRcate
DMRcate
14 months ago Bazingastats • 0
0
votes
0
replies
632
views
DMR.plot "Error: Too many stacks to draw"
DMRcate Gviz GV
14 months ago gilliangoobie • 0
2
votes
6
replies
1.7k
views
DMRcate
DMRcate R DMRcatedata Markdown
14 months ago yr542 • 0
0
votes
0
replies
834
views
How to increase font for gene name and increase arrow size for GVIZ's ( UcscTrack function ) track?
DMRcate Gviz
2.4 years ago Ahdee ▴ 50
0
votes
1
reply
913
views
Same error that DMRcate Error in if (nsig == 0) { : missing value where TRUE/FALSE needed
DMRcate
updated 2.5 years ago by 65k • written 2.5 years ago by ▴ 30
0
votes
2
replies
971
views
DMRcate: how to compare two comparisons and whether replicate is necessary
DMRcate WGBS biological_replicate
2.6 years ago xie186 • 0
0
votes
6
replies
1.3k
views
Find genes in pathways enrichment
dmrcate enrichment analysis epic array goregion missmethyl
updated 2.8 years ago by ▴ 10 • written 3.8 years ago by ▴ 10
1
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2
replies
1.5k
views
DMRcate extractRanges error
DMRcate
3.2 years ago macsue.jacques ▴ 10
0
votes
0
replies
748
views
DMRcate shows incorrect overlapping non-coding RNA genes
DMRcate
3.4 years ago Mike ▴ 10
3
votes
4
replies
1.0k
views
Is it possible to run DMRcate directly with genomic positions instead of probe names?
DMRcate
updated 3.6 years ago by ▴ 180 • written 3.6 years ago by ▴ 10
0
votes
2
replies
794
views
The smoothed Y statistic is far elevated from limma Y statistic, and parameter "betacutoff" never used
dmrcate
3.8 years ago zh9118 • 0
4
votes
9
replies
3.0k
views
DMRcate Error in if (nsig == 0) { : missing value where TRUE/FALSE needed
DMRcate differencial methylation
updated 2.5 years ago by ▴ 30 • written 3.9 years ago by ▴ 10
1
vote
8
replies
1.8k
views
extract CpGs from DMRcate results
dmrcate cpgs results.ranges DMRcate
updated 4.0 years ago by ▴ 180 • written 4.0 years ago by ▴ 40
3
votes
5
replies
1.4k
views
DMRcate: Cpgids in DMR
methylation Epic annotation DMRcate
updated 4.6 years ago by 65k • written 4.6 years ago by ▴ 10
0
votes
3
replies
1.4k
views
Significant DMRs in genes with no single significant CpG using limma
DMRcate
updated 4.7 years ago by ▴ 180 • written 4.7 years ago by • 0
0
votes
2
replies
1.2k
views
cpg.annotate model requirements
DMRcate ChAMP
updated 4.8 years ago by ▴ 280 • written 4.8 years ago by • 0
1
vote
3
replies
1.3k
views
DMRcate liftover to grch38
hg19 liftover matrixeqtl DMRcate
updated 4.9 years ago by 65k • written 4.9 years ago by ▴ 10
2
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18
replies
4.9k
views
DMRcate results cg ID of significant DMR
dmrcate
updated 5.8 years ago by • 0 • written 7.9 years ago by ▴ 160
0
votes
3
replies
1.6k
views
DMRcate package :How to find the gene associated with coordinate
dmrcate gene symbol coordinate
5.8 years ago 574233829 • 0
2
votes
6
replies
1.9k
views
Bumphunting for longitudinal data
bumphunter minfi lmer dmrcate dmr analysis
updated 6.0 years ago by ▴ 180 • written 6.0 years 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
1
vote
2
replies
1.5k
views
DMRcate results file ordered by genomic location and not Stouffer p-val?
DMRcate dmrcate methylation
updated 6.9 years ago by ▴ 180 • written 6.9 years ago by • 0
1
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3
replies
1.5k
views
coef in dmrcate
dmrcate bumphunter methylation epic
updated 7.0 years ago by 65k • written 7.0 years ago by ▴ 10
0
votes
11
replies
3.8k
views
bug in cpg.annotate() and DMR.plot: bad defaults for what and arraytype arguments
DMRcate minfi
updated 3 months ago by ▴ 180 • written 7.1 years ago by ★ 2.0k
1
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10
replies
3.0k
views
minfi, lumi, methylumi, DMRcate installation error
minfi lumi methylumi dmrcate illuminahumanmethylation450kanno.ilmn12.hg19
updated 7.1 years ago by ▴ 180 • written 7.1 years ago by ▴ 10
0
votes
1
reply
1.5k
views
DMRcate: Scaling factor for bandwidth
dmrcate dmr analysis dmr
updated 7.3 years ago by ▴ 180 • written 7.3 years ago by ▴ 10
0
votes
2
replies
1.4k
views
DMRcate DMR.plot Turn Off Group Means
dmrcate visualization
updated 7.3 years ago by ▴ 180 • written 7.3 years ago by • 0
1
vote
2
replies
1.1k
views
DMRcate error in extractCoords function
software error DMRcate extractRanges
updated 7.3 years ago by ▴ 180 • written 7.3 years ago by ▴ 10
0
votes
1
reply
986
views
Betacutoff is not used in dmrcate function.
DMRcate
updated 7.3 years ago by ▴ 180 • written 7.3 years ago by • 0
0
votes
9
replies
19k
views
dmrcate(): Error in `$<-.data.frame`(`*tmp*`, "sig", value = logical(0)) : replacement has 0 rows, data has 1963
dmrcate
updated 7.3 years ago by ▴ 180 • written 7.5 years ago by • 0
1
vote
15
replies
2.3k
views
DMRcate results meanpvals
dmrcate
updated 7.8 years ago by ▴ 180 • written 7.9 years ago by ▴ 160
0
votes
1
reply
981
views
conflicts in chromosome number
DMRcate
updated 7.9 years ago by ▴ 180 • written 7.9 years ago by • 0
2
votes
2
replies
1.7k
views
DMRcate error: object 'annotated' not found
dmrcate error
updated 8.4 years ago by ▴ 180 • written 8.4 years ago by • 0
0
votes
5
replies
2.2k
views
DMRcate cpg.annotate error: "Error in data.frame"
dmrcate
8.4 years ago par.larsson • 0
2
votes
2
replies
2.4k
views
DMRcate cpg.annotate error
dmrcate design matrix
updated 8.5 years ago by ▴ 180 • written 8.5 years ago by ▴ 160
1
vote
1
reply
1.4k
views
DMRcate: phenotype variable with multiple levels
dmr analysis dmrcate
updated 8.8 years ago by ▴ 370 • written 8.8 years ago by • 0
0
votes
3
replies
3.1k
views
DMRcate: incorporating covariates to find DMRs in methylation data?
limma illimina 450k methylation DMRcate
updated 9.1 years ago by ▴ 180 • written 9.1 years ago by ▴ 120
50 results • Page 1 of 1
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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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