Showing : DMRcate • reset
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470
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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
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0
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449
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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
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Significant DMRs in genes with no single significant CpG using limma
DMRcate
written 6.3 years ago by • 0
0
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1
reply
574
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No preprocessing allowed for EPICv2 with DMRcate
missMethyl DMRcate
updated 10 months ago by 68k • written 10 months ago by • 0
0
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1
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1.7k
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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 4.0 years ago by ▴ 60
2
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4
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885
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
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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
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511
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Limma Interaction Effect with Covariates
limma DMRcate
12 months ago kitzhu • 0
0
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0
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450
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DMRcate pcutoff setting
EpicV2 DMRcate
13 months ago kitzhu • 0
4
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12
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5.8k
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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
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2
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1.1k
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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
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2
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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
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0
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664
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DMRcate error need at least two non-NA values to interpolate
DNAMethylation DMRcate
20 months ago Macsue • 0
1
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2
replies
3.0k
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EPIC array hg38 annotation?
minfi DMRcate
21 months ago mycetes • 0
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0
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554
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What is the significance of DMR in DMRcate
DMRcate
22 months ago chuanjiao6 • 0
3
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2
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796
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Question about DMRcate
DMRcate dmrcate
22 months ago chuanjiao6 • 0
8
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7
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2.3k
views
Why is DMRcate not available for Bioconductor version 3.18?
DMRcate
written 24 months ago by ▴ 30
0
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5
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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
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1
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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
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4
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1.8k
views
DMRcate design
Epigenetics EpigeneticsWorkflow DMRcate
2.2 years ago Jitendra ▴ 10
0
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1
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1.1k
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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
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6
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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
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12
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3.1k
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Error when loading DMRcate
DMRcate
2.8 years ago Bazingastats • 0
0
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0
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1.2k
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DMR.plot "Error: Too many stacks to draw"
DMRcate Gviz GV
2.8 years ago gilliangoobie • 0
2
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6
replies
2.8k
views
DMRcate
DMRcate R DMRcatedata Markdown
2.8 years ago yr542 • 0
0
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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
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6
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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
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2.1k
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DMRcate extractRanges error
DMRcate
4.7 years ago macsue.jacques ▴ 10
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0
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1.1k
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DMRcate shows incorrect overlapping non-coding RNA genes
DMRcate
5.0 years ago Mike ▴ 10
3
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4
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1.7k
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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
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2
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1.3k
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The smoothed Y statistic is far elevated from limma Y statistic, and parameter "betacutoff" never used
dmrcate
5.3 years ago zh9118 • 0
4
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9
replies
4.1k
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 6.1 years ago by 68k • written 6.1 years ago by ▴ 10
0
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2
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1.8k
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cpg.annotate model requirements
DMRcate ChAMP
updated 6.3 years ago by ▴ 290 • written 6.3 years ago by • 0
1
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3
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1.8k
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DMRcate liftover to grch38
hg19 liftover matrixeqtl DMRcate
updated 6.5 years ago by 68k • written 6.5 years ago by ▴ 10
2
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18
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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
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3
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2.2k
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DMRcate package :How to find the gene associated with coordinate
dmrcate gene symbol coordinate
7.4 years ago 574233829 • 0
2
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6
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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
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3
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2.5k
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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
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2
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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
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3
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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
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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
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1
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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
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2
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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
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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
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1
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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 `$<-.data.frame`(`*tmp*`, "sig", value = logical(0)) : replacement has 0 rows, data has 1963
dmrcate
updated 8.9 years ago by ▴ 230 • written 9.1 years ago by • 0
1
vote
15
replies
3.3k
views
DMRcate results meanpvals
dmrcate
updated 9.4 years ago by ▴ 230 • written 9.4 years ago by ▴ 160
56 results • Page 1 of 2
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Replies
Comment: upstream git branches of bioc-release by TrentonCollier99 • 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments. https://bioc-release.r-univ…
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Ahmed Salah • 0
Thank you very much! will take that into consideration
Comment: Large logFC but somewhat high FDR by JKim • 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments.
Comment: upstream git branches of bioc-release by Jeroen ▴ 10
OK I have updated https://bioc-release.r-universe.dev accordingly. Let me know if you find version differences when mirroring binaries.
Comment: Large logFC but somewhat high FDR by Gordon Smyth 53k
I don't know what `tp1` is. The relevant histogram would be: ``` hist(fit2$p.value[,"KO_vs_WT"]) ```
Votes
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
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
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