Bioconductor DNA Methylation

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1.2k

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minfi cell proportion estimateCellCounts DNA Methylation

5.0 years ago grayapply2009 • 0

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2.5k

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normalization DNA methylation WGCNA

updated 5.7 years ago by Peter Langfelder ★ 3.0k • written 5.7 years ago by enora.fremy • 0

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1.2k

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medips medip-seq dna methylation dmr analysis

updated 6.3 years ago by Lukas Chavez ▴ 570 • written 6.3 years ago by mtefit • 0

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1.9k

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R gdc rna-seq dna methylation

updated 6.4 years ago by Sean Davis 21k • written 6.4 years ago by RichardJActon ▴ 50

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1.6k

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minfi normalization outliers dna methylation densityplot

6.6 years ago peter.fransquet • 0

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909

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differential variability dna methylation iEVORA DVP

6.8 years ago poojitha.stemcell ▴ 10

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1.2k

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rnbeads methylation methylationepic dna methylation

7.0 years ago gabrielrfries • 0

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1.3k

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dna methylation biseq

updated 7.2 years ago by Gordon Smyth 52k • written 7.2 years ago by ahmad.moousavi • 0

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2.2k

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tcgabiolinks dna methylation

updated 7.3 years ago by Marcel Ramos 700 • written 7.3 years ago by michaelwxf2012 • 0

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2.1k

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dna methylation illimina 450k methylation beta M significance

updated 7.4 years ago by James W. MacDonald 68k • written 7.4 years ago by skids121 • 0

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1.4k

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CNV minfi preprocessing dna methylation

7.9 years ago Thomas • 0

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1.2k

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microarray HM450 dna methylation cohcap

updated 8.1 years ago by James W. MacDonald 68k • written 8.1 years ago by poojitha.stemcell ▴ 10

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1.3k

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minfi bumphunter DNA methylation illumina450k

updated 8.7 years ago by James W. MacDonald 68k • written 8.7 years ago by fleur_p90 • 0

13 results • Page 1 of 1

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Comment: Use of limma R package with targeted proteomics for DE analysis by svlachavas ▴ 840

Dear Gordon, thank you for returning back ! Actually the output is not "NPX"-as indeed it most frequent output for a lot of pannels-but as …

Comment: how many significant figures are there in DESeq2 output by ATpoint ★ 4.7k

If you want consistency then use a fixed software environment like Docker, wirh fixed code and thresholds that make sense. Rounding to near…

Comment: Compare TCGA-PAAD with GTEx gene expression by Jane • 0

why aren't there any answers?

Comment: Too many significant genes when integrating gtex and tcga by Jane • 0

I encountered the same issue: too many DEGs after limma analysis. It is sad that until today we can still see the paper published where GTE…

Comment: how many significant figures are there in DESeq2 output by Matthew McCormack ▴ 180

Thank you for your reply. It is good to know that cutoff of 0.05 means less than 0.05. My concerns are about consistency and reproducibili…

Votes

Comment: Use of limma R package with targeted proteomics for DE analysis

A: Unbalanced experiment with multiple samples from each patient.

Unbalanced experiment with multiple samples from each patient.

Answer: Vertical line at A=0, nothing else, on MA plot

Answer: GSVA Error Code "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct

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