Showing : dmrcate • reset
0
votes
1
reply
96
views
No preprocessing allowed for EPICv2 with DMRcate
missMethyl DMRcate
updated 20 days ago by 67k • written 20 days ago by • 0
0
votes
1
reply
1.3k
views
How to increase font for gene name and increase arrow size for GVIZ's ( UcscTrack function ) track?
DMRcate Gviz
updated 25 days ago by • 0 • written 3.1 years ago by ▴ 50
2
votes
4
replies
482
views
Can we get beta values with DMRcate package
DMRcatedata DMRcate
7 weeks ago • updated 6 weeks ago Melisa Tecik • 0
0
votes
7
replies
617
views
how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
minfi DMRcate
updated 3 days ago by 67k • written 8 weeks ago by • 0
1
vote
2
replies
246
views
Limma Interaction Effect with Covariates
limma DMRcate
10 weeks ago kitzhu • 0
0
votes
0
replies
217
views
DMRcate pcutoff setting
EpicV2 DMRcate
3 months ago kitzhu • 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
3
votes
2
replies
823
views
limma Intercept vs No-intercept models completely changing DMR results?
limma DMRcate MethylationArray EPICV2
updated 8 months ago by 52k • written 8 months ago by • 0
1
vote
2
replies
1.7k
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 9 months ago by ▴ 200 • written 23 months ago by ▴ 10
0
votes
0
replies
380
views
DMRcate error need at least two non-NA values to interpolate
DNAMethylation DMRcate
9 months ago Macsue • 0
1
vote
2
replies
2.0k
views
EPIC array hg38 annotation?
minfi DMRcate
11 months ago mycetes • 0
0
votes
0
replies
363
views
What is the significance of DMR in DMRcate
DMRcate
11 months ago chuanjiao6 • 0
3
votes
2
replies
524
views
Question about DMRcate
DMRcate dmrcate
12 months ago chuanjiao6 • 0
8
votes
7
replies
1.9k
views
Why is DMRcate not available for Bioconductor version 3.18?
DMRcate
written 14 months ago by ▴ 30
0
votes
5
replies
960
views
error while running DMRcate
stattistics epicarray Epigenetics DMRcate
updated 15 months ago by 67k • written 15 months ago by ▴ 10
0
votes
1
reply
1.0k
views
DMR.plot() Error in .local(.Object, ...) : Failed to obtain 'hguid' cookie
DMRcate DMR.plot
updated 15 months ago by 4.1k • written 15 months ago by • 0
3
votes
4
replies
1.4k
views
DMRcate design
Epigenetics EpigeneticsWorkflow DMRcate
16 months ago Jitendra ▴ 10
0
votes
1
reply
811
views
dmrcate needs at least two non-NA values to interpolate
miss DMRcate missMethyl
updated 17 months ago by ▴ 200 • written 17 months ago by • 0
2
votes
6
replies
1.5k
views
cpg.annotate() in DMRcate error
DNAMethylation methylationArrayAnalysis DMRcate MethylationArrayData MethylationArray
updated 21 months ago by ▴ 200 • written 21 months ago by • 0
6
votes
12
replies
2.5k
views
Error when loading DMRcate
DMRcate
23 months ago Bazingastats • 0
0
votes
0
replies
929
views
DMR.plot "Error: Too many stacks to draw"
DMRcate Gviz GV
23 months ago gilliangoobie • 0
2
votes
6
replies
2.3k
views
DMRcate
DMRcate R DMRcatedata Markdown
23 months ago yr542 • 0
0
votes
1
reply
1.2k
views
Same error that DMRcate Error in if (nsig == 0) { : missing value where TRUE/FALSE needed
DMRcate
updated 3.2 years ago by 67k • written 3.2 years ago by ▴ 30
0
votes
6
replies
1.6k
views
Find genes in pathways enrichment
dmrcate enrichment analysis epic array goregion missmethyl
updated 3.5 years ago by ▴ 20 • written 4.5 years ago by ▴ 10
1
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2
replies
1.8k
views
DMRcate extractRanges error
DMRcate
3.9 years ago macsue.jacques ▴ 10
0
votes
0
replies
936
views
DMRcate shows incorrect overlapping non-coding RNA genes
DMRcate
4.2 years ago Mike ▴ 10
3
votes
4
replies
1.4k
views
Is it possible to run DMRcate directly with genomic positions instead of probe names?
DMRcate
updated 4.3 years ago by ▴ 200 • written 4.3 years ago by ▴ 10
0
votes
2
replies
973
views
The smoothed Y statistic is far elevated from limma Y statistic, and parameter "betacutoff" never used
dmrcate
4.5 years ago zh9118 • 0
4
votes
9
replies
3.6k
views
DMRcate Error in if (nsig == 0) { : missing value where TRUE/FALSE needed
DMRcate differencial methylation
updated 3.2 years ago by ▴ 30 • written 4.6 years ago by ▴ 10
1
vote
8
replies
2.5k
views
extract CpGs from DMRcate results
dmrcate cpgs results.ranges DMRcate
updated 4.7 years ago by ▴ 200 • written 4.7 years ago by ▴ 40
3
votes
5
replies
1.7k
views
DMRcate: Cpgids in DMR
methylation Epic annotation DMRcate
updated 5.3 years ago by 67k • written 5.3 years ago by ▴ 10
0
votes
3
replies
2.1k
views
Significant DMRs in genes with no single significant CpG using limma
DMRcate
updated 5.5 years ago by ▴ 200 • written 5.5 years ago by • 0
0
votes
2
replies
1.5k
views
cpg.annotate model requirements
DMRcate ChAMP
updated 5.5 years ago by ▴ 290 • written 5.5 years ago by • 0
1
vote
3
replies
1.5k
views
DMRcate liftover to grch38
hg19 liftover matrixeqtl DMRcate
updated 5.7 years ago by 67k • written 5.7 years ago by ▴ 10
2
votes
18
replies
5.7k
views
DMRcate results cg ID of significant DMR
dmrcate
updated 6.6 years ago by • 0 • written 8.7 years ago by ▴ 160
0
votes
3
replies
1.9k
views
DMRcate package :How to find the gene associated with coordinate
dmrcate gene symbol coordinate
6.6 years ago 574233829 • 0
2
votes
6
replies
2.3k
views
Bumphunting for longitudinal data
bumphunter minfi lmer dmrcate dmr analysis
updated 6.7 years ago by ▴ 200 • written 6.7 years ago by • 0
0
votes
3
replies
2.2k
views
error in champ.DMR using DMRcate (v2.8.3)
champ dmrcate IlluminaHumanMethylationEPICanno.ilm10b2.hg19
updated 7.6 years ago by ▴ 90 • written 7.6 years ago by • 0
1
vote
2
replies
1.8k
views
DMRcate results file ordered by genomic location and not Stouffer p-val?
DMRcate dmrcate methylation
updated 7.7 years ago by ▴ 200 • written 7.7 years ago by • 0
1
vote
3
replies
1.8k
views
coef in dmrcate
dmrcate bumphunter methylation epic
updated 7.8 years ago by 67k • written 7.8 years ago by ▴ 10
0
votes
11
replies
4.6k
views
bug in cpg.annotate() and DMR.plot: bad defaults for what and arraytype arguments
DMRcate minfi
updated 12 months ago by ▴ 200 • written 7.8 years ago by ★ 2.0k
1
vote
10
replies
3.5k
views
minfi, lumi, methylumi, DMRcate installation error
minfi lumi methylumi dmrcate illuminahumanmethylation450kanno.ilmn12.hg19
updated 7.9 years ago by ▴ 200 • written 7.9 years ago by ▴ 10
0
votes
1
reply
1.8k
views
DMRcate: Scaling factor for bandwidth
dmrcate dmr analysis dmr
updated 8.0 years ago by ▴ 200 • written 8.0 years ago by ▴ 10
0
votes
2
replies
1.7k
views
DMRcate DMR.plot Turn Off Group Means
dmrcate visualization
updated 8.0 years ago by ▴ 200 • written 8.0 years ago by • 0
1
vote
2
replies
1.4k
views
DMRcate error in extractCoords function
software error DMRcate extractRanges
updated 8.0 years ago by ▴ 200 • written 8.0 years ago by ▴ 10
0
votes
1
reply
1.1k
views
Betacutoff is not used in dmrcate function.
DMRcate
updated 8.0 years ago by ▴ 200 • written 8.1 years ago by • 0
0
votes
9
replies
20k
views
dmrcate(): Error in `$<-.data.frame`(`*tmp*`, "sig", value = logical(0)) : replacement has 0 rows, data has 1963
dmrcate
updated 8.1 years ago by ▴ 200 • written 8.3 years ago by • 0
1
vote
15
replies
2.8k
views
DMRcate results meanpvals
dmrcate
updated 8.6 years ago by ▴ 200 • written 8.6 years ago by ▴ 160
0
votes
1
reply
1.1k
views
conflicts in chromosome number
DMRcate
updated 8.6 years ago by ▴ 200 • written 8.6 years ago by • 0
2
votes
2
replies
2.0k
views
DMRcate error: object 'annotated' not found
dmrcate error
updated 9.1 years ago by ▴ 200 • written 9.1 years ago by • 0
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Answer: Selection of correct coefficients or contrasts in DESeq2 by swbarnes2 ★ 1.4k
I think you need to include the design you used, and the command you used to call it. The simplest answer is that your two ways of doing t…
Comment: Csaw normalization strategies - general inquiry by Luca • 0
Hello Aaron, About the IP efficiencies, yes definitely and for us, to complicate this experiment further, these batches were generated by …
Comment: How to compare expression levels of genes between scRNAseq and bulkRNAseq? by Quang NN ▴ 10
Thank you ATpoint for your response. In bulkRNAseq, I did have two cell types to compare. But, I want to also see if bulkRNAseq might have …
Answer: Why select top highly expressed genes based on normalized counts, but then plot by ATpoint ★ 4.6k
The choice of variable genes is typically part of a QC process. You select genes that in an unbiased fashion (unbiased because variance cal…
Comment: How to compare expression levels of genes between scRNAseq and bulkRNAseq? by ATpoint ★ 4.6k
My take is that RNA-seq (be it bulk or single-cell) is inherently relative. I don't think you can really "compare" the absolute expression …
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Answer: Csaw normalization strategies - general inquiry
A: DESeq2 interaction term
Comment: Recount3 data correspond to TCGA data
Answer: DESeq2- merging technical vs biological replicates
Answer: SingleCellExperiment convenience function for metadata+expression?
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