Showing : dmrcate • reset
0
votes
1
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468
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Filtering out non-variable probes from EPICv2 matrix
DMRcate EPICv2manifest
updated 6 months ago by 68k • written 6 months ago by • 0
0
votes
0
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437
views
Significant Probes and Genes differ in Probe and Region level Differential Methylation Analyses
limma probe DMRcate GenomicRanges DifferentialMethylation
6 months ago jamiecatalano2 • 0
0
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4
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2.8k
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Significant DMRs in genes with no single significant CpG using limma
DMRcate
written 6.3 years ago by • 0
0
votes
1
reply
569
views
No preprocessing allowed for EPICv2 with DMRcate
missMethyl DMRcate
updated 10 months ago by 68k • written 10 months ago by • 0
0
votes
1
reply
1.7k
views
How to increase font for gene name and increase arrow size for GVIZ's ( UcscTrack function ) track?
DMRcate Gviz
updated 10 months ago by • 0 • written 3.9 years ago by ▴ 60
2
votes
4
replies
873
views
Can we get beta values with DMRcate package
DMRcatedata DMRcate
11 months ago Melisa Tecik • 0
4
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8
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1.8k
views
how to apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
DMRcate minfi
11 months ago • updated 8 months ago xiaofeiwang198266 • 0
1
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2
replies
502
views
Limma Interaction Effect with Covariates
limma DMRcate
12 months ago kitzhu • 0
0
votes
0
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445
views
DMRcate pcutoff setting
EpicV2 DMRcate
13 months ago kitzhu • 0
4
votes
12
replies
5.7k
views
How to get DMR for Infinium methylation EPIC v2
ChAMP DMRcate minfi
updated 15 months ago by ▴ 230 • written 24 months ago by ▴ 20
3
votes
2
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1.1k
views
limma Intercept vs No-intercept models completely changing DMR results?
limma DMRcate MethylationArray EPICV2
updated 17 months ago by 53k • written 18 months ago by • 0
1
vote
2
replies
2.3k
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 19 months ago by ▴ 230 • written 2.7 years ago by ▴ 10
0
votes
0
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657
views
DMRcate error need at least two non-NA values to interpolate
DNAMethylation DMRcate
19 months ago Macsue • 0
1
vote
2
replies
3.0k
views
EPIC array hg38 annotation?
minfi DMRcate
21 months ago mycetes • 0
0
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0
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548
views
What is the significance of DMR in DMRcate
DMRcate
21 months ago chuanjiao6 • 0
3
votes
2
replies
782
views
Question about DMRcate
DMRcate dmrcate
21 months ago chuanjiao6 • 0
8
votes
7
replies
2.3k
views
Why is DMRcate not available for Bioconductor version 3.18?
DMRcate
written 23 months ago by ▴ 30
0
votes
5
replies
1.3k
views
error while running DMRcate
stattistics epicarray Epigenetics DMRcate
updated 2.1 years ago by 68k • written 2.1 years ago by ▴ 10
0
votes
1
reply
1.2k
views
DMR.plot() Error in .local(.Object, ...) : Failed to obtain 'hguid' cookie
DMRcate DMR.plot
updated 2.1 years ago by 4.2k • written 2.1 years ago by • 0
3
votes
4
replies
1.8k
views
DMRcate design
Epigenetics EpigeneticsWorkflow DMRcate
2.1 years ago Jitendra ▴ 10
0
votes
1
reply
1.1k
views
dmrcate needs at least two non-NA values to interpolate
miss DMRcate missMethyl
updated 2.3 years ago by ▴ 230 • written 2.3 years ago by • 0
2
votes
6
replies
1.9k
views
cpg.annotate() in DMRcate error
DNAMethylation methylationArrayAnalysis DMRcate MethylationArrayData MethylationArray
updated 2.6 years ago by ▴ 230 • written 2.6 years ago by • 0
6
votes
12
replies
3.1k
views
Error when loading DMRcate
DMRcate
2.7 years ago Bazingastats • 0
0
votes
0
replies
1.2k
views
DMR.plot "Error: Too many stacks to draw"
DMRcate Gviz GV
2.8 years ago gilliangoobie • 0
2
votes
6
replies
2.8k
views
DMRcate
DMRcate R DMRcatedata Markdown
2.8 years ago yr542 • 0
0
votes
1
reply
1.4k
views
Same error that DMRcate Error in if (nsig == 0) { : missing value where TRUE/FALSE needed
DMRcate
updated 4.0 years ago by 68k • written 4.0 years ago by ▴ 30
0
votes
6
replies
2.0k
views
Find genes in pathways enrichment
dmrcate enrichment analysis epic array goregion missmethyl
updated 4.3 years ago by ▴ 20 • written 5.3 years ago by ▴ 10
1
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2
replies
2.0k
views
DMRcate extractRanges error
DMRcate
4.7 years ago macsue.jacques ▴ 10
0
votes
0
replies
1.1k
views
DMRcate shows incorrect overlapping non-coding RNA genes
DMRcate
5.0 years ago Mike ▴ 10
3
votes
4
replies
1.7k
views
Is it possible to run DMRcate directly with genomic positions instead of probe names?
DMRcate
updated 5.1 years ago by ▴ 230 • written 5.1 years ago by ▴ 10
0
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2
replies
1.3k
views
The smoothed Y statistic is far elevated from limma Y statistic, and parameter "betacutoff" never used
dmrcate
5.3 years ago zh9118 • 0
4
votes
9
replies
4.1k
views
DMRcate Error in if (nsig == 0) { : missing value where TRUE/FALSE needed
DMRcate differencial methylation
updated 4.0 years ago by ▴ 30 • written 5.4 years ago by ▴ 10
1
vote
8
replies
3.1k
views
extract CpGs from DMRcate results
dmrcate cpgs results.ranges DMRcate
updated 5.5 years ago by ▴ 230 • written 5.5 years ago by ▴ 40
3
votes
5
replies
2.1k
views
DMRcate: Cpgids in DMR
methylation Epic annotation DMRcate
updated 6.1 years ago by 68k • written 6.1 years ago by ▴ 10
0
votes
2
replies
1.8k
views
cpg.annotate model requirements
DMRcate ChAMP
updated 6.3 years ago by ▴ 290 • written 6.3 years ago by • 0
1
vote
3
replies
1.8k
views
DMRcate liftover to grch38
hg19 liftover matrixeqtl DMRcate
updated 6.5 years ago by 68k • written 6.5 years ago by ▴ 10
2
votes
18
replies
7.0k
views
DMRcate results cg ID of significant DMR
dmrcate
updated 7.4 years ago by • 0 • written 9.5 years ago by ▴ 160
0
votes
3
replies
2.2k
views
DMRcate package :How to find the gene associated with coordinate
dmrcate gene symbol coordinate
7.4 years ago 574233829 • 0
2
votes
6
replies
2.7k
views
Bumphunting for longitudinal data
bumphunter minfi lmer dmrcate dmr analysis
updated 7.5 years ago by ▴ 230 • written 7.5 years ago by • 0
0
votes
3
replies
2.5k
views
error in champ.DMR using DMRcate (v2.8.3)
champ dmrcate IlluminaHumanMethylationEPICanno.ilm10b2.hg19
updated 8.4 years ago by ▴ 90 • written 8.4 years ago by • 0
1
vote
2
replies
2.1k
views
DMRcate results file ordered by genomic location and not Stouffer p-val?
DMRcate dmrcate methylation
updated 8.5 years ago by ▴ 230 • written 8.5 years ago by • 0
1
vote
3
replies
2.0k
views
coef in dmrcate
dmrcate bumphunter methylation epic
updated 8.6 years ago by 68k • written 8.6 years ago by ▴ 10
0
votes
11
replies
5.4k
views
bug in cpg.annotate() and DMR.plot: bad defaults for what and arraytype arguments
DMRcate minfi
updated 21 months ago by ▴ 230 • written 8.6 years ago by ★ 2.0k
1
vote
10
replies
4.0k
views
minfi, lumi, methylumi, DMRcate installation error
minfi lumi methylumi dmrcate illuminahumanmethylation450kanno.ilmn12.hg19
updated 8.7 years ago by ▴ 230 • written 8.7 years ago by ▴ 10
0
votes
1
reply
2.0k
views
DMRcate: Scaling factor for bandwidth
dmrcate dmr analysis dmr
updated 8.8 years ago by ▴ 230 • written 8.8 years ago by ▴ 10
0
votes
2
replies
1.9k
views
DMRcate DMR.plot Turn Off Group Means
dmrcate visualization
updated 8.8 years ago by ▴ 230 • written 8.8 years ago by • 0
1
vote
2
replies
1.5k
views
DMRcate error in extractCoords function
software error DMRcate extractRanges
updated 8.8 years ago by ▴ 230 • written 8.8 years ago by ▴ 10
0
votes
1
reply
1.3k
views
Betacutoff is not used in dmrcate function.
DMRcate
updated 8.8 years ago by ▴ 230 • written 8.8 years ago by • 0
0
votes
9
replies
22k
views
dmrcate(): Error in `$<-.data.frame`(`*tmp*`, "sig", value = logical(0)) : replacement has 0 rows, data has 1963
dmrcate
updated 8.9 years ago by ▴ 230 • written 9.1 years ago by • 0
1
vote
15
replies
3.3k
views
DMRcate results meanpvals
dmrcate
updated 9.4 years ago by ▴ 230 • written 9.4 years ago by ▴ 160
56 results • Page 1 of 2
Recent ...
Replies
Comment: Getting a large intercept with DESeq2 by Michael Love 43k
Thanks James -- Denise you can check the "note on factor levels" in the vignette. And I'd recommend `plotCounts()` for looking at individu…
Comment: Getting a large intercept with DESeq2 by James W. MacDonald 68k
As a trivial example, consider this: ``` > model.matrix(~Treatment, data.frame(Treatment = factor(rep(1:3, each = 4)))) (Intercept) Tre…
Answer: Getting a large intercept with DESeq2 by James W. MacDonald 68k
The default parameterization in R is a treatment-contrasts parameterization that sets one of your groups as the baseline. So the intercept …
Answer: Must I do pseudobulk analysis on Cell Surface Protein Labeling data of Single C by ATpoint ★ 5.0k
There is no "MUST", but pseudobulk aggregation is beneficial to a) enable use of tested and robust methods such as limma (though it could u…
Answer: Post translational modifications and phosphoproteomics in limpa? by Gordon Smyth 53k
Yes, we use limpa for PTMs ourselves. I assume your data is preprocessed so that each row corresponds to a PTM. You replace dpcQuant() with…
Votes
Answer: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif
Using edgeR or DESeq2 to analyze allele-specific expression?
Answer: DESeq2 design for haplotype MPRA
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Failure to download resources (MeSHDb) from AnnotationHub
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