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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570
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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
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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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366
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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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935
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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
0
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1
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817
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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
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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
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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910
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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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849
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missmethyl gsameth outputs matrix instead of dataframe
missmethyl gsameth
5.9 years ago owen.whitley ▴ 10
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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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910
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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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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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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
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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
views
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
views
Pathway analysis of differentially methylated CpGs
limma 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
3
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3
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3.5k
views
missMethyl: Gene ontology analysis
missMethyl
8.1 years ago philipp24 ▴ 30
23 results • Page 1 of 1
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Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
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!
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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