Showing : DMRcate • reset
0
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9
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19k
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dmrcate(): Error in `$<-.data.frame`(`*tmp*`, "sig", value = logical(0)) : replacement has 0 rows, data has 1963
dmrcate
updated 7.3 years ago by ▴ 170 • written 7.5 years ago by • 0
2
votes
18
replies
4.9k
views
DMRcate results cg ID of significant DMR
dmrcate
updated 5.8 years ago by • 0 • written 7.9 years ago by ▴ 160
0
votes
11
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3.7k
views
bug in cpg.annotate() and DMR.plot: bad defaults for what and arraytype arguments
DMRcate minfi
updated 12 weeks ago by ▴ 170 • written 7.1 years ago by ★ 2.0k
0
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3
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3.1k
views
DMRcate: incorporating covariates to find DMRs in methylation data?
limma illimina 450k methylation DMRcate
updated 9.0 years ago by ▴ 170 • written 9.0 years ago by ▴ 120
1
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10
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3.0k
views
minfi, lumi, methylumi, DMRcate installation error
minfi lumi methylumi dmrcate illuminahumanmethylation450kanno.ilmn12.hg19
updated 7.1 years ago by ▴ 170 • written 7.1 years ago by ▴ 10
4
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9
replies
3.0k
views
DMRcate Error in if (nsig == 0) { : missing value where TRUE/FALSE needed
DMRcate differencial methylation
updated 2.5 years ago by ▴ 30 • written 3.9 years ago by ▴ 10
2
votes
2
replies
2.4k
views
DMRcate cpg.annotate error
dmrcate design matrix
updated 8.4 years ago by ▴ 170 • written 8.4 years ago by ▴ 160
1
vote
15
replies
2.3k
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DMRcate results meanpvals
dmrcate
updated 7.8 years ago by ▴ 170 • written 7.8 years ago by ▴ 160
0
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5
replies
2.1k
views
DMRcate cpg.annotate error: "Error in data.frame"
dmrcate
8.4 years ago par.larsson • 0
0
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3
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1.9k
views
error in champ.DMR using DMRcate (v2.8.3)
champ dmrcate IlluminaHumanMethylationEPICanno.ilm10b2.hg19
updated 6.8 years ago by ▴ 90 • written 6.8 years ago by • 0
2
votes
6
replies
1.8k
views
Bumphunting for longitudinal data
bumphunter minfi lmer dmrcate dmr analysis
updated 6.0 years ago by ▴ 170 • written 6.0 years ago by • 0
1
vote
8
replies
1.8k
views
extract CpGs from DMRcate results
dmrcate cpgs results.ranges DMRcate
updated 3.9 years ago by ▴ 170 • written 3.9 years ago by ▴ 40
6
votes
12
replies
1.7k
views
Error when loading DMRcate
DMRcate
14 months ago Bazingastats • 0
2
votes
6
replies
1.7k
views
DMRcate
DMRcate R DMRcatedata Markdown
14 months ago yr542 • 0
2
votes
2
replies
1.6k
views
DMRcate error: object 'annotated' not found
dmrcate error
updated 8.4 years ago by ▴ 170 • written 8.4 years ago by • 0
0
votes
3
replies
1.6k
views
DMRcate package :How to find the gene associated with coordinate
dmrcate gene symbol coordinate
5.8 years ago 574233829 • 0
1
vote
2
replies
1.5k
views
DMRcate results file ordered by genomic location and not Stouffer p-val?
DMRcate dmrcate methylation
updated 6.9 years ago by ▴ 170 • written 6.9 years ago by • 0
1
vote
3
replies
1.5k
views
coef in dmrcate
dmrcate bumphunter methylation epic
updated 7.0 years ago by 65k • written 7.0 years ago by ▴ 10
0
votes
1
reply
1.5k
views
DMRcate: Scaling factor for bandwidth
dmrcate dmr analysis dmr
updated 7.2 years ago by ▴ 170 • written 7.2 years ago by ▴ 10
1
vote
2
replies
1.5k
views
DMRcate extractRanges error
DMRcate
3.2 years ago • updated 3.1 years ago macsue.jacques ▴ 10
1
vote
1
reply
1.4k
views
DMRcate: phenotype variable with multiple levels
dmr analysis dmrcate
updated 8.7 years ago by ▴ 370 • written 8.7 years ago by • 0
0
votes
2
replies
1.4k
views
DMRcate DMR.plot Turn Off Group Means
dmrcate visualization
updated 7.3 years ago by ▴ 170 • written 7.3 years ago by • 0
3
votes
5
replies
1.4k
views
DMRcate: Cpgids in DMR
methylation Epic annotation DMRcate
updated 4.5 years ago by 65k • written 4.6 years ago by ▴ 10
0
votes
3
replies
1.3k
views
Significant DMRs in genes with no single significant CpG using limma
DMRcate
updated 4.7 years ago by ▴ 170 • written 4.7 years ago by • 0
2
votes
6
replies
1.3k
views
How to get DMR for Infinium methylation EPIC v2
ChAMP DMRcate minfi
updated 22 days ago by ▴ 170 • written 5 months ago by ▴ 10
0
votes
6
replies
1.3k
views
Find genes in pathways enrichment
dmrcate enrichment analysis epic array goregion missmethyl
updated 2.8 years ago by ▴ 10 • written 3.8 years ago by ▴ 10
1
vote
3
replies
1.2k
views
DMRcate liftover to grch38
hg19 liftover matrixeqtl DMRcate
updated 4.9 years ago by 65k • written 4.9 years ago by ▴ 10
0
votes
2
replies
1.2k
views
cpg.annotate model requirements
DMRcate ChAMP
updated 4.8 years ago by ▴ 280 • written 4.8 years ago by • 0
1
vote
2
replies
1.1k
views
DMRcate error in extractCoords function
software error DMRcate extractRanges
updated 7.3 years ago by ▴ 170 • written 7.3 years ago by ▴ 10
8
votes
7
replies
1.1k
views
Why is DMRcate not available for Bioconductor version 3.18?
DMRcate
written 4 months ago by ▴ 30
2
votes
6
replies
1.1k
views
cpg.annotate() in DMRcate error
DNAMethylation methylationArrayAnalysis DMRcate MethylationArrayData MethylationArray
updated 12 months ago by ▴ 170 • written 12 months ago by • 0
3
votes
4
replies
1.0k
views
Is it possible to run DMRcate directly with genomic positions instead of probe names?
DMRcate
updated 3.6 years ago by ▴ 170 • written 3.6 years ago by ▴ 10
0
votes
1
reply
976
views
Betacutoff is not used in dmrcate function.
DMRcate
updated 7.3 years ago by ▴ 170 • written 7.3 years ago by • 0
0
votes
1
reply
970
views
conflicts in chromosome number
DMRcate
updated 7.8 years ago by ▴ 170 • written 7.8 years ago by • 0
0
votes
2
replies
945
views
DMRcate: how to compare two comparisons and whether replicate is necessary
DMRcate WGBS biological_replicate
2.6 years ago xie186 • 0
1
vote
2
replies
925
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 2 days ago by ▴ 170 • written 14 months ago by ▴ 10
0
votes
1
reply
890
views
Same error that DMRcate Error in if (nsig == 0) { : missing value where TRUE/FALSE needed
DMRcate
updated 2.5 years ago by 65k • written 2.5 years ago by ▴ 30
3
votes
4
replies
826
views
DMRcate design
Epigenetics EpigeneticsWorkflow DMRcate
7 months ago Jitendra ▴ 10
0
votes
0
replies
824
views
How to increase font for gene name and increase arrow size for GVIZ's ( UcscTrack function ) track?
DMRcate Gviz
2.4 years ago Ahdee ▴ 50
0
votes
2
replies
786
views
The smoothed Y statistic is far elevated from limma Y statistic, and parameter "betacutoff" never used
dmrcate
3.7 years ago zh9118 • 0
0
votes
0
replies
741
views
DMRcate shows incorrect overlapping non-coding RNA genes
DMRcate
3.4 years ago Mike ▴ 10
0
votes
1
reply
727
views
DMR.plot() Error in .local(.Object, ...) : Failed to obtain 'hguid' cookie
DMRcate DMR.plot
updated 6 months ago by 3.8k • written 6 months ago by • 0
0
votes
0
replies
620
views
DMR.plot "Error: Too many stacks to draw"
DMRcate Gviz GV
14 months ago gilliangoobie • 0
0
votes
5
replies
590
views
error while running DMRcate
stattistics epicarray Epigenetics DMRcate
updated 6 months ago by 65k • written 6 months ago by ▴ 10
0
votes
1
reply
466
views
dmrcate needs at least two non-NA values to interpolate
miss DMRcate missMethyl
updated 8 months ago by ▴ 170 • written 8 months ago by • 0
0
votes
2
replies
453
views
EPIC array hg38 annotation?
minfi DMRcate
10 weeks ago mycetes • 0
3
votes
2
replies
261
views
Question about DMRcate
DMRcate dmrcate
12 weeks ago • updated 11 weeks ago chuanjiao6 • 0
0
votes
0
replies
123
views
What is the significance of DMR in DMRcate
DMRcate
11 weeks ago chuanjiao6 • 0
0
votes
0
replies
78
views
DMRcate error need at least two non-NA values to interpolate
DNAMethylation DMRcate
21 days ago Macsue • 0
49 results • Page 1 of 1
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Comment: How to retrieve gene ontology GO class from gene list? by bandconductor • 0
Thanks, this is potentially a much faster way than parsing BiomRt. However, it is only returning one GO term right now (biomaRt returns a f…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Comment: PCA plot suggestions by JKim • 0
cross post: https://www.biostars.org/p/9593486/
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
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