Showing : dmrcate • reset
0
votes
1
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477
views
Filtering out non-variable probes from EPICv2 matrix
DMRcate EPICv2manifest
updated 7 months ago by 68k • written 7 months ago by • 0
0
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0
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456
views
Significant Probes and Genes differ in Probe and Region level Differential Methylation Analyses
limma probe DMRcate GenomicRanges DifferentialMethylation
7 months ago jamiecatalano2 • 0
0
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4
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2.8k
views
Significant DMRs in genes with no single significant CpG using limma
DMRcate
written 6.3 years ago by • 0
0
votes
1
reply
576
views
No preprocessing allowed for EPICv2 with DMRcate
missMethyl DMRcate
updated 11 months ago by 68k • written 11 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 11 months ago by • 0 • written 4.0 years ago by ▴ 60
2
votes
4
replies
886
views
Can we get beta values with DMRcate package
DMRcatedata DMRcate
12 months ago • updated 11 months ago Melisa Tecik • 0
4
votes
8
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1.8k
views
how to apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
DMRcate minfi
12 months ago • updated 9 months ago xiaofeiwang198266 • 0
1
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2
replies
515
views
Limma Interaction Effect with Covariates
limma DMRcate
12 months ago kitzhu • 0
0
votes
0
replies
453
views
DMRcate pcutoff setting
EpicV2 DMRcate
14 months ago kitzhu • 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
3
votes
2
replies
1.1k
views
limma Intercept vs No-intercept models completely changing DMR results?
limma DMRcate MethylationArray EPICV2
updated 18 months ago by 53k • written 19 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 2.8 years ago by ▴ 10
0
votes
0
replies
668
views
DMRcate error need at least two non-NA values to interpolate
DNAMethylation DMRcate
20 months ago Macsue • 0
1
vote
2
replies
3.0k
views
EPIC array hg38 annotation?
minfi DMRcate
22 months ago mycetes • 0
0
votes
0
replies
557
views
What is the significance of DMR in DMRcate
DMRcate
22 months ago chuanjiao6 • 0
3
votes
2
replies
803
views
Question about DMRcate
DMRcate dmrcate
22 months ago chuanjiao6 • 0
8
votes
7
replies
2.3k
views
Why is DMRcate not available for Bioconductor version 3.18?
DMRcate
written 2.0 years 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
2.2 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
2.8 years ago Bazingastats • 0
0
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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 4.1 years ago by 68k • written 4.1 years ago by ▴ 30
0
votes
6
replies
2.0k
views
Find genes in pathways enrichment
dmrcate enrichment analysis epic array goregion missmethyl
updated 4.4 years ago by ▴ 20 • written 5.4 years ago by ▴ 10
1
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2
replies
2.1k
views
DMRcate extractRanges error
DMRcate
4.8 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 5.2 years ago by ▴ 230 • written 5.2 years ago by ▴ 10
0
votes
2
replies
1.3k
views
The smoothed Y statistic is far elevated from limma Y statistic, and parameter "betacutoff" never used
dmrcate
5.4 years ago zh9118 • 0
4
votes
9
replies
4.2k
views
DMRcate Error in if (nsig == 0) { : missing value where TRUE/FALSE needed
DMRcate differencial methylation
updated 4.1 years ago by ▴ 30 • written 5.5 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 6.2 years ago by 68k • written 6.2 years ago by ▴ 10
0
votes
2
replies
1.8k
views
cpg.annotate model requirements
DMRcate ChAMP
updated 6.4 years ago by ▴ 290 • written 6.4 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 7.6 years ago by ▴ 230 • written 7.6 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 8.5 years ago by ▴ 90 • written 8.5 years ago by • 0
1
vote
2
replies
2.2k
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 22 months ago by ▴ 230 • written 8.7 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 8.9 years ago by ▴ 10
0
votes
2
replies
1.9k
views
DMRcate DMR.plot Turn Off Group Means
dmrcate visualization
updated 8.9 years ago by ▴ 230 • written 8.9 years ago by • 0
1
vote
2
replies
1.5k
views
DMRcate error in extractCoords function
software error DMRcate extractRanges
updated 8.9 years ago by ▴ 230 • written 8.9 years ago by ▴ 10
0
votes
1
reply
1.3k
views
Betacutoff is not used in dmrcate function.
DMRcate
updated 8.9 years ago by ▴ 230 • written 8.9 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
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…
Answer: Question about DESeq2 Design for Paired Treatment Study by ATpoint ★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Comment: problem reading bam files into nucleR by efoss ▴ 10
I thought I might be able to track down a problematic line in the bam file by repeatedly splitting the bam file in and then running the co…
Answer: two questions about limma by Gordon Smyth 53k
Answered here: https://support.bioconductor.org/p/16318/
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
Commentator to sina.nassiri ▴ 130
Popular Question to Hervé Pagès 16k
Popular Question to jared.andrews07 ▴ 30
Popular Question to James W. MacDonald 68k
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