Showing : dmrcate • reset
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Significant DMRs in genes with no single significant CpG using limma
DMRcate
written 5.7 years ago by • 0
0
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1
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306
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No preprocessing allowed for EPICv2 with DMRcate
missMethyl DMRcate
updated 3 months ago by 68k • written 3 months ago by • 0
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1
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1.5k
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How to increase font for gene name and increase arrow size for GVIZ's ( UcscTrack function ) track?
DMRcate Gviz
updated 3 months ago by • 0 • written 3.4 years ago by ▴ 60
2
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4
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639
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Can we get beta values with DMRcate package
DMRcatedata DMRcate
4 months ago Melisa Tecik • 0
4
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8
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1.3k
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how to apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
DMRcate minfi
4 months ago • updated 9 weeks ago xiaofeiwang198266 • 0
1
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2
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352
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Limma Interaction Effect with Covariates
limma DMRcate
5 months ago kitzhu • 0
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305
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DMRcate pcutoff setting
EpicV2 DMRcate
6 months ago kitzhu • 0
4
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12
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4.9k
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How to get DMR for Infinium methylation EPIC v2
ChAMP DMRcate minfi
updated 9 months ago by ▴ 230 • written 17 months ago by ▴ 20
3
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2
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923
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limma Intercept vs No-intercept models completely changing DMR results?
limma DMRcate MethylationArray EPICV2
updated 10 months ago by 52k • written 11 months ago by • 0
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2
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1.9k
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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 months ago by ▴ 230 • written 2.2 years ago by ▴ 10
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490
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DMRcate error need at least two non-NA values to interpolate
DNAMethylation DMRcate
12 months ago Macsue • 0
1
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2
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2.5k
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EPIC array hg38 annotation?
minfi DMRcate
14 months ago mycetes • 0
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0
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426
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What is the significance of DMR in DMRcate
DMRcate
14 months ago chuanjiao6 • 0
3
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2
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586
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Question about DMRcate
DMRcate dmrcate
15 months ago • updated 14 months ago chuanjiao6 • 0
8
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7
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2.1k
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Why is DMRcate not available for Bioconductor version 3.18?
DMRcate
written 17 months ago by ▴ 30
0
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5
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1.1k
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error while running DMRcate
stattistics epicarray Epigenetics DMRcate
updated 18 months ago by 68k • written 18 months ago by ▴ 10
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1
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1.1k
views
DMR.plot() Error in .local(.Object, ...) : Failed to obtain 'hguid' cookie
DMRcate DMR.plot
updated 18 months ago by 4.1k • written 18 months ago by • 0
3
votes
4
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1.6k
views
DMRcate design
Epigenetics EpigeneticsWorkflow DMRcate
19 months ago Jitendra ▴ 10
0
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1
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913
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dmrcate needs at least two non-NA values to interpolate
miss DMRcate missMethyl
updated 20 months ago by ▴ 230 • written 20 months ago by • 0
2
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6
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1.7k
views
cpg.annotate() in DMRcate error
DNAMethylation methylationArrayAnalysis DMRcate MethylationArrayData MethylationArray
updated 2.0 years ago by ▴ 230 • written 2.0 years ago by • 0
6
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12
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2.7k
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Error when loading DMRcate
DMRcate
2.2 years ago Bazingastats • 0
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1.0k
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DMR.plot "Error: Too many stacks to draw"
DMRcate Gviz GV
2.2 years ago gilliangoobie • 0
2
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6
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2.5k
views
DMRcate
DMRcate R DMRcatedata Markdown
2.2 years ago yr542 • 0
0
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1
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1.2k
views
Same error that DMRcate Error in if (nsig == 0) { : missing value where TRUE/FALSE needed
DMRcate
updated 3.5 years ago by 68k • written 3.5 years ago by ▴ 30
0
votes
6
replies
1.7k
views
Find genes in pathways enrichment
dmrcate enrichment analysis epic array goregion missmethyl
updated 3.8 years ago by ▴ 20 • written 4.8 years ago by ▴ 10
1
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2
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1.9k
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DMRcate extractRanges error
DMRcate
4.2 years ago • updated 4.1 years ago macsue.jacques ▴ 10
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1.0k
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DMRcate shows incorrect overlapping non-coding RNA genes
DMRcate
4.4 years ago Mike ▴ 10
3
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4
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1.5k
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Is it possible to run DMRcate directly with genomic positions instead of probe names?
DMRcate
updated 4.6 years ago by ▴ 230 • written 4.6 years ago by ▴ 10
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2
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1.1k
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The smoothed Y statistic is far elevated from limma Y statistic, and parameter "betacutoff" never used
dmrcate
4.7 years ago zh9118 • 0
4
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9
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3.8k
views
DMRcate Error in if (nsig == 0) { : missing value where TRUE/FALSE needed
DMRcate differencial methylation
updated 3.5 years ago by ▴ 30 • written 4.9 years ago by ▴ 10
1
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8
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2.8k
views
extract CpGs from DMRcate results
dmrcate cpgs results.ranges DMRcate
updated 4.9 years ago by ▴ 230 • written 4.9 years ago by ▴ 40
3
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5
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1.8k
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DMRcate: Cpgids in DMR
methylation Epic annotation DMRcate
updated 5.6 years ago by 68k • written 5.6 years ago by ▴ 10
0
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2
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1.6k
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cpg.annotate model requirements
DMRcate ChAMP
updated 5.8 years ago by ▴ 290 • written 5.8 years ago by • 0
1
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3
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1.6k
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DMRcate liftover to grch38
hg19 liftover matrixeqtl DMRcate
updated 5.9 years ago by 68k • written 5.9 years ago by ▴ 10
2
votes
18
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6.3k
views
DMRcate results cg ID of significant DMR
dmrcate
updated 6.8 years ago by • 0 • written 8.9 years ago by ▴ 160
0
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3
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2.0k
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DMRcate package :How to find the gene associated with coordinate
dmrcate gene symbol coordinate
6.8 years ago 574233829 • 0
2
votes
6
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2.4k
views
Bumphunting for longitudinal data
bumphunter minfi lmer dmrcate dmr analysis
updated 7.0 years ago by ▴ 230 • written 7.0 years ago by • 0
0
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3
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2.4k
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error in champ.DMR using DMRcate (v2.8.3)
champ dmrcate IlluminaHumanMethylationEPICanno.ilm10b2.hg19
updated 7.8 years ago by ▴ 90 • written 7.8 years ago by • 0
1
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2
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2.0k
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DMRcate results file ordered by genomic location and not Stouffer p-val?
DMRcate dmrcate methylation
updated 7.9 years ago by ▴ 230 • written 7.9 years ago by • 0
1
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3
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1.9k
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coef in dmrcate
dmrcate bumphunter methylation epic
updated 8.0 years ago by 68k • written 8.0 years ago by ▴ 10
0
votes
11
replies
5.0k
views
bug in cpg.annotate() and DMR.plot: bad defaults for what and arraytype arguments
DMRcate minfi
updated 15 months ago by ▴ 230 • written 8.1 years ago by ★ 2.0k
1
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10
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3.7k
views
minfi, lumi, methylumi, DMRcate installation error
minfi lumi methylumi dmrcate illuminahumanmethylation450kanno.ilmn12.hg19
updated 8.1 years ago by ▴ 230 • written 8.1 years ago by ▴ 10
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1
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1.8k
views
DMRcate: Scaling factor for bandwidth
dmrcate dmr analysis dmr
updated 8.2 years ago by ▴ 230 • written 8.2 years ago by ▴ 10
0
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2
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1.8k
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DMRcate DMR.plot Turn Off Group Means
dmrcate visualization
updated 8.3 years ago by ▴ 230 • written 8.3 years ago by • 0
1
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2
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1.4k
views
DMRcate error in extractCoords function
software error DMRcate extractRanges
updated 8.3 years ago by ▴ 230 • written 8.3 years ago by ▴ 10
0
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1
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1.2k
views
Betacutoff is not used in dmrcate function.
DMRcate
updated 8.3 years ago by ▴ 230 • written 8.3 years ago by • 0
0
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9
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21k
views
dmrcate(): Error in `$<-.data.frame`(`*tmp*`, "sig", value = logical(0)) : replacement has 0 rows, data has 1963
dmrcate
updated 8.3 years ago by ▴ 230 • written 8.5 years ago by • 0
1
vote
15
replies
2.9k
views
DMRcate results meanpvals
dmrcate
updated 8.8 years ago by ▴ 230 • written 8.8 years ago by ▴ 160
0
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1
reply
1.2k
views
conflicts in chromosome number
DMRcate
updated 8.8 years ago by ▴ 230 • written 8.8 years ago by • 0
2
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2
replies
2.1k
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DMRcate error: object 'annotated' not found
dmrcate error
updated 9.4 years ago by ▴ 230 • written 9.4 years ago by • 0
50 results • Page 1 of 1
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Comment: error in ChAMP loading file by janwilseo • 0
Any update on this post? I also had an issue with this. [erosion control](https://charlestonhydroseeding.com/)
Answer: CluserProfiler message "No gene can be mapped" by James W. MacDonald 68k
Two things. First, the order of your term2gene is backwards (should be term and then gene, like the name), and by default `enricher` adjust…
Comment: Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis by donnycrimson • 0
One potential workaround might be to adjust for these factors using a combination of design matrices perhaps including batch as a covariate…
Comment: DESeq2 Design controlling for gender by donnycrimson • 0
On a lighter note, while you are tackling such complex data, you might enjoy a quick break playing the [Slope Game](https://slopegame.lol)…
Comment: MetaDE.pvalue: Error in xj[i]: invalid subscript type 'list' by donnycrimson • 0
Have you considered streamlining how you handle data input to mitigate these issues. It might help to define the parameters more strictly …
Votes
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
A: Understanding contrasts limma
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