Showing : MethylationArrayData • reset
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Mismatch between Illumina Mouse Methylation BeadChip annotation and genome browsers (UCSC/Ensembl)
methylationArrayAnalysis MethylationArrayData
updated 8 months ago by 68k • written 8 months ago by • 0
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480
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Conumee for EPIC and EPICv2 copy number
conumee CopyNumberVariation MethylationArrayData
9 months ago • updated 8 months ago Adam • 0
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Methylation data - different probes are classified differently based on transcript? (Illumina methylation arrays, using minfi)
minf minfiDataEPIC MethylationArrayData MethylationArray EPICv2manifest
9 months ago charlie.wright • 0
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Meffil: error in functional normalization function (Error in rg.to.mu(rg, probes))
methylationArrayAnalysis Normalization Epigenetics MethylationArrayData
9 months ago a.alkema • 0
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Unable to find sample sheet file for ChAMP methylation data analysis
MethylationArray MethylationArrayData methylationArrayAnalysis
updated 10 months ago by 68k • written 10 months ago by • 0
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697
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Annotating DMRs
MethylationArray MethylationArrayData methylationArrayAnalysis
updated 14 months ago by 68k • written 14 months ago by ▴ 10
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TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray normalize450K TCGAbiolinks Normalization MethylationArrayData
21 months ago • updated 20 months ago Giovanni Calice ▴ 160
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Normalization in methylation analysis
Methylation minfi preprocessQuantile MethylationArrayData preprocessFunnorm
23 months ago kyj2226 • 0
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Methylation data analysis
MethylationArrayData methylationArrayAnalysis
2.0 years ago aldea85 • 0
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Merging Methylation data (M-values) with phenotypic data
MethylationArrayData methylationArrayAnalysis
updated 2.3 years ago by 68k • written 2.3 years ago by • 0
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Read methylation data from tar files on GEO (GSE73303)
GeneExpression Bioconductor GEOquery MethylationArrayData
2.3 years ago Arianna • 0
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1.4k
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How to perform a methylation analyisis from m values
MethylationArrayData methylationArrayAnalysis
2.5 years ago Irene • 0
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1
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1.0k
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urgent error for producing table of topGO() annotated DMPs methylation
methylationArrayAnalysis topGO missMethyl MethylationArrayData MethylationArray
updated 2.6 years ago by ▴ 40 • written 2.6 years ago by • 0
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1.9k
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cpg.annotate() in DMRcate error
DNAMethylation methylationArrayAnalysis DMRcate MethylationArrayData MethylationArray
updated 2.6 years ago by ▴ 230 • written 2.6 years ago by • 0
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1.1k
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LmFit error in EPIC methylation array analysis, Minfi
methylationArrayAnalysis minfi MethylationArrayData minfiDataEPIC MethylationArray
updated 2.6 years ago by 53k • written 2.7 years ago by • 0
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Sex estimation problems in [estimateCellCounts]: methylation arrays
methylationArrayAnalysis minfiData minfi MethylationArrayData MethylationArray
updated 2.7 years ago by 68k • written 2.7 years ago by • 0
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2.3k
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minfi error read.metharray.exp
methylationArrayAnalysis minfiData minfi MethylationArrayData MethylationArray
written 2.7 years ago by • 0
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2
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2.5k
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ChAMP package:Error in cmdscale(d) : 'k' must be in {1, 2, .. n - 1}
MethylationArrayData
3.1 years ago shuangshuang • 0
2
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2
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1.9k
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Limma vs. lm for methylation data
limma MethylationArrayData MethylationArray
3.6 years ago fluentin44 • 0
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1.1k
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filtering options in RnBeads for array data
Epigenetics RnBeads MethylationArrayData methylationArrayAnalysis
3.7 years ago Jitendra ▴ 10
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1.3k
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Problem loading Red channel idat files with champ.load
R MethylationArrayData ChAMP
4.0 years ago Paulina • 0
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1.2k
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DNA methylation EPIC array and ChromHMM
chromhmmData MethylationArrayData
4.3 years ago macsue.jacques ▴ 10
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1.2k
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minfi - estimateCellCounts2-proportions sum more than 1
minfi minfiData MethylationArrayData
4.3 years ago ponche_de_kiwi • 0
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6
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4.8k
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Merge problems in R
methylationArrayAnalysis ChAMP MethylationArrayData
4.4 years ago FWNL15 • 0
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1
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1.3k
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Error in reading metharray sheet
DifferentialMethylation MethylationArrayData
updated 4.5 years ago by ▴ 780 • written 4.5 years ago by • 0
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1.6k
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How to get illumina CpG IDs by gene name?
MethylationArrayData RnBeads
4.7 years ago D ▴ 10
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4
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3.8k
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Unable to read in the IDAT files using read.metharray.exp()
MethylationArrayData methy Bioconductor minfi
4.8 years ago shweta • 0
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1
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3.3k
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DMR Plot
dmr MethylationArrayData DMRcatedata
updated 5.1 years ago by 68k • written 5.1 years ago by • 0
28 results • Page 1 of 1
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Comment: Large logFC but somewhat high FDR by JKim • 0
Thank you very much for taking the time to leave a reply. 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"]) ```
Answer: p.adjust BH Question by Gordon Smyth 53k
Duplicate of https://support.bioconductor.org/p/41077/
Answer: Large logFC but somewhat high FDR by Gordon Smyth 53k
Glad you're getting good use out of the package. The results that you show seem pretty much as one would expect, with nothing surprising. …
Votes
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
A: p.adjust BH generates duplicate values
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