Showing : missmethyl • reset
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256
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Error in GOmeth function of missMethyl when EPICv2 annotation is used
DNAMethylation GO MethylationArray missMethyl EPICv2
updated 8 weeks ago by ▴ 40 • written 8 weeks ago by • 0
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1
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480
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dmrcate needs at least two non-NA values to interpolate
miss DMRcate missMethyl
updated 8 months ago by ▴ 180 • written 8 months ago by • 0
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2
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569
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ageData (minfi pipeline)
ageData missMethyl differentialvariability minfi
updated 5 weeks ago by • 0 • written 11 months ago by • 0
1
vote
1
reply
562
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urgent error for producing table of topGO() annotated DMPs methylation
methylationArrayAnalysis topGO missMethyl MethylationArrayData MethylationArray
updated 12 months ago by ▴ 40 • written 12 months ago by • 0
0
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1
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494
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topGO() analysis of DMPs in missMethyl methylation analysis
DNAMethylation missMethyl Pathways
12 months ago Grace • 0
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0
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365
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goMeth
missMethyl
13 months ago anmolanp ▴ 10
2
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6
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950
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No enriched GO terms CpGs
DNAMethylation missMethyl
updated 14 months ago by ▴ 40 • written 14 months ago by • 0
2
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3
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934
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GSEA for paired methylation data
missMethyl GSEA minfi methylGSA
updated 16 months ago by ▴ 40 • written 16 months ago by • 0
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6
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1.3k
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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
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1
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816
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missMethyl - get names of differentially methylated genes from gometh()
missMethyl
updated 2.8 years ago by ▴ 10 • written 3.7 years ago by ▴ 10
1
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2
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2.0k
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Minfi read.metharray.sheet error
minfi methylation dataimport minfidata missmethyl
updated 5.6 years ago by 65k • written 5.6 years ago by ▴ 20
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0
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908
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missMethyl EPIC manifest update
missmethyl epic illuminahumanmethylationepicanno.ilm10b4.hg19. ruv
5.7 years ago peter.fransquet • 0
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0
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849
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missmethyl gsameth outputs matrix instead of dataframe
missmethyl gsameth
5.8 years ago owen.whitley ▴ 10
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1
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1.3k
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Test for differential variability with missMethyl (DiffVar) using block design
missmethyl diffvar design matrix limma block
updated 6.0 years ago by ▴ 50 • written 6.9 years ago by ▴ 190
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895
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which value from ruvadj in missMethyl can present methylation status
methylation missmethyl RUV batch effect
6.0 years ago RC • 0
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0
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909
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MissMethyl: Sample size and control probes
missmethyl RUV control probes
6.0 years ago Taub, Margaret ▴ 10
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2
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1.4k
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prior.prob has opposite effects in goana and kegga?
limma missMethyl gometh goana kegga
updated 6.8 years ago by 50k • written 7.0 years ago by ★ 2.0k
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3
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1.3k
views
Details of gene names in DE
missmethyl
updated 7.1 years ago by 65k • written 7.1 years ago by • 0
0
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1
reply
1.2k
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missMethyl package: gsameth bias plots
missmethyl plots bias package
updated 7.2 years ago by ▴ 40 • written 7.2 years ago by • 0
1
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2
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1.4k
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Gene Ontology Overrepresentation Analysis with a custom level of Abstraction of GO Terminology
gene ontology GO overrepresentation analysis missmethyl gostats
updated 7.7 years ago by 65k • written 7.7 years ago by • 0
1
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3
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3.0k
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Pathway analysis of differentially methylated CpGs
limma missmethyl
8.1 years ago philipp24 ▴ 30
3
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3
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3.5k
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missMethyl: Gene ontology analysis
missMethyl
8.1 years ago philipp24 ▴ 30
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0
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1.2k
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Pathway analysis of differentially methylated CpGs
limma missmethyl
8.1 years ago philipp24 ▴ 30
23 results • Page 1 of 1
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Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0
Thank you Tim, this is a great help in getting me started!
Comment: Too many significant genes when integrating gtex and tcga by Michael Love 41k
Yes, this was one of the aspects we highlighted in the 2014 paper, and it's also in the workflow. Check these places first. Also take a st…
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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