Bioconductor GenomeStudio

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beadarray Illuminabeadchip GenomeStudio lumi

6 months ago • updated 5 months ago Liu • 0

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minfi genomestudio methylation

updated 8.0 years ago by James W. MacDonald 68k • written 8.0 years ago by brhead ▴ 40

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GWASTools qualitycontrol HumanOmni5-4BeadChip GenomeStudio illumina

updated 9.0 years ago by Stephanie M. Gogarten ▴ 890 • written 9.0 years ago by Lna • 0

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Comment: parameters of filterByExpr by caroline.zanchi ▴ 10

It worked, I think I finally understand and accept that fact. Sorry and thank you again !

Comment: parameters of filterByExpr by Gordon Smyth 52k

You seem to be coming back to the same fixed (but incorrect) idea of what filterByExpr() should be doing. I have tried to explain that filt…

Answer: edgeR in DMR mode - replicates give batch effect - how to build design matrix wi by Gordon Smyth 52k

modelMatrixMeth() works correctly. The second replicate factor has not been lost. Please do not make ad hoc manual modifications to the de…

Comment: Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatm by James W. MacDonald 68k

Probably not. Any given gene may be appended with many different GO terms, so you would end up with something that is not very useful. ``…

Comment: Heatmap of rnaseq data with z-score scale by James W. MacDonald 68k

`heatmap.2` is a CRAN package, and that's the relevant issue for this plot. It's got nothing to do with `DESeq2` or any other Bioconductor …

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Answer: LogFC values in edgeR - w/wo intercept

How to formulate 2 factor nested design in DESeq2

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