Showing : dmrcate • reset
2
votes
4
replies
382
views
Can we get beta values with DMRcate package
DMRcatedata DMRcate
11 days ago • updated 10 days ago Melisa Tecik • 0
0
votes
5
replies
344
views
how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
minfi DMRcate
18 days ago • updated 1 day ago xiaofeiwang198266 • 0
0
votes
2
replies
170
views
Limma Interaction Effect with Covariates
limma DMRcate
4 weeks ago kitzhu • 0
0
votes
0
replies
176
views
DMRcate pcutoff setting
EpicV2 DMRcate
10 weeks ago kitzhu • 0
3
votes
12
replies
3.8k
views
How to get DMR for Infinium methylation EPIC v2
ChAMP DMRcate minfi
updated 4 months ago by ▴ 200 • written 13 months ago by ▴ 10
3
votes
2
replies
787
views
limma Intercept vs No-intercept models completely changing DMR results?
limma DMRcate MethylationArray EPICV2
updated 6 months ago by 52k • written 7 months ago by • 0
1
vote
2
replies
1.6k
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 8 months ago by ▴ 200 • written 22 months ago by ▴ 10
0
votes
0
replies
343
views
DMRcate error need at least two non-NA values to interpolate
DNAMethylation DMRcate
8 months ago Macsue • 0
1
vote
2
replies
1.8k
views
EPIC array hg38 annotation?
minfi DMRcate
10 months ago mycetes • 0
0
votes
0
replies
338
views
What is the significance of DMR in DMRcate
DMRcate
10 months ago chuanjiao6 • 0
3
votes
2
replies
498
views
Question about DMRcate
DMRcate dmrcate
10 months ago chuanjiao6 • 0
8
votes
7
replies
1.9k
views
Why is DMRcate not available for Bioconductor version 3.18?
DMRcate
written 12 months ago by ▴ 30
0
votes
5
replies
918
views
error while running DMRcate
stattistics epicarray Epigenetics DMRcate
updated 14 months ago by 67k • written 14 months ago by ▴ 10
0
votes
1
reply
996
views
DMR.plot() Error in .local(.Object, ...) : Failed to obtain 'hguid' cookie
DMRcate DMR.plot
updated 14 months ago by 4.1k • written 14 months ago by • 0
3
votes
4
replies
1.4k
views
DMRcate design
Epigenetics EpigeneticsWorkflow DMRcate
15 months ago Jitendra ▴ 10
0
votes
1
reply
777
views
dmrcate needs at least two non-NA values to interpolate
miss DMRcate missMethyl
updated 16 months ago by ▴ 200 • written 16 months ago by • 0
2
votes
6
replies
1.5k
views
cpg.annotate() in DMRcate error
DNAMethylation methylationArrayAnalysis DMRcate MethylationArrayData MethylationArray
updated 20 months ago by ▴ 200 • written 20 months ago by • 0
6
votes
12
replies
2.4k
views
Error when loading DMRcate
DMRcate
22 months ago Bazingastats • 0
0
votes
0
replies
897
views
DMR.plot "Error: Too many stacks to draw"
DMRcate Gviz GV
22 months ago gilliangoobie • 0
2
votes
6
replies
2.2k
views
DMRcate
DMRcate R DMRcatedata Markdown
22 months ago yr542 • 0
0
votes
0
replies
1.2k
views
How to increase font for gene name and increase arrow size for GVIZ's ( UcscTrack function ) track?
DMRcate Gviz
3.0 years ago Ahdee ▴ 50
0
votes
1
reply
1.1k
views
Same error that DMRcate Error in if (nsig == 0) { : missing value where TRUE/FALSE needed
DMRcate
updated 3.1 years ago by 67k • written 3.1 years ago by ▴ 30
0
votes
2
replies
1.4k
views
DMRcate: how to compare two comparisons and whether replicate is necessary
DMRcate WGBS biological_replicate
3.2 years ago xie186 • 0
0
votes
6
replies
1.6k
views
Find genes in pathways enrichment
dmrcate enrichment analysis epic array goregion missmethyl
updated 3.4 years ago by ▴ 20 • written 4.4 years ago by ▴ 10
1
vote
2
replies
1.8k
views
DMRcate extractRanges error
DMRcate
3.8 years ago macsue.jacques ▴ 10
0
votes
0
replies
916
views
DMRcate shows incorrect overlapping non-coding RNA genes
DMRcate
4.1 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 4.2 years ago by ▴ 200 • written 4.2 years ago by ▴ 10
0
votes
2
replies
952
views
The smoothed Y statistic is far elevated from limma Y statistic, and parameter "betacutoff" never used
dmrcate
4.4 years ago zh9118 • 0
4
votes
9
replies
3.5k
views
DMRcate Error in if (nsig == 0) { : missing value where TRUE/FALSE needed
DMRcate differencial methylation
updated 3.1 years ago by ▴ 30 • written 4.5 years ago by ▴ 10
1
vote
8
replies
2.4k
views
extract CpGs from DMRcate results
dmrcate cpgs results.ranges DMRcate
updated 4.6 years ago by ▴ 200 • written 4.6 years ago by ▴ 40
3
votes
5
replies
1.7k
views
DMRcate: Cpgids in DMR
methylation Epic annotation DMRcate
updated 5.2 years ago by 67k • written 5.2 years ago by ▴ 10
0
votes
3
replies
2.0k
views
Significant DMRs in genes with no single significant CpG using limma
DMRcate
updated 5.4 years ago by ▴ 200 • written 5.4 years ago by • 0
0
votes
2
replies
1.4k
views
cpg.annotate model requirements
DMRcate ChAMP
updated 5.4 years ago by ▴ 290 • written 5.4 years ago by • 0
1
vote
3
replies
1.5k
views
DMRcate liftover to grch38
hg19 liftover matrixeqtl DMRcate
updated 5.6 years ago by 67k • written 5.6 years ago by ▴ 10
2
votes
18
replies
5.6k
views
DMRcate results cg ID of significant DMR
dmrcate
updated 6.5 years ago by • 0 • written 8.6 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
6.5 years ago 574233829 • 0
2
votes
6
replies
2.2k
views
Bumphunting for longitudinal data
bumphunter minfi lmer dmrcate dmr analysis
updated 6.6 years ago by ▴ 200 • written 6.6 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 7.5 years ago by ▴ 90 • written 7.5 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 7.6 years ago by ▴ 200 • written 7.6 years ago by • 0
1
vote
3
replies
1.7k
views
coef in dmrcate
dmrcate bumphunter methylation epic
updated 7.7 years ago by 67k • written 7.7 years ago by ▴ 10
0
votes
11
replies
4.5k
views
bug in cpg.annotate() and DMR.plot: bad defaults for what and arraytype arguments
DMRcate minfi
updated 10 months ago by ▴ 200 • written 7.7 years ago by ★ 2.0k
1
vote
10
replies
3.4k
views
minfi, lumi, methylumi, DMRcate installation error
minfi lumi methylumi dmrcate illuminahumanmethylation450kanno.ilmn12.hg19
updated 7.8 years ago by ▴ 200 • written 7.8 years ago by ▴ 10
0
votes
1
reply
1.7k
views
DMRcate: Scaling factor for bandwidth
dmrcate dmr analysis dmr
updated 7.9 years ago by ▴ 200 • written 7.9 years ago by ▴ 10
0
votes
2
replies
1.7k
views
DMRcate DMR.plot Turn Off Group Means
dmrcate visualization
updated 7.9 years ago by ▴ 200 • written 7.9 years ago by • 0
1
vote
2
replies
1.3k
views
DMRcate error in extractCoords function
software error DMRcate extractRanges
updated 7.9 years ago by ▴ 200 • written 7.9 years ago by ▴ 10
0
votes
1
reply
1.1k
views
Betacutoff is not used in dmrcate function.
DMRcate
updated 7.9 years ago by ▴ 200 • written 7.9 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 8.0 years ago by ▴ 200 • written 8.2 years ago by • 0
1
vote
15
replies
2.7k
views
DMRcate results meanpvals
dmrcate
updated 8.5 years ago by ▴ 200 • written 8.5 years ago by ▴ 160
0
votes
1
reply
1.1k
views
conflicts in chromosome number
DMRcate
updated 8.5 years ago by ▴ 200 • written 8.5 years ago by • 0
2
votes
2
replies
1.9k
views
DMRcate error: object 'annotated' not found
dmrcate error
updated 9.0 years ago by ▴ 200 • written 9.0 years ago by • 0
50 results • Page 1 of 1
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Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by xiaofeiwang198266 • 0
Thanks for your reply!
Votes
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
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