User: Greg Finak

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Greg Finak50
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Posts by Greg Finak

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automating makeContrasts call in limma
... The following line should do what you want. > myContrasts<-c("t1-t2","t1-3","t2-t3") contrast.matrix <- eval(as.call(c(as.symbol("makeContrasts"),as.list (myContrasts),levels=list(design)))) It's the same convention as making calls to R functions through C code. Cheers, On 11-Mar-06, a ...
go written 11.5 years ago by Greg Finak50
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Answer: A: Rocke-Lorenzato model or Global Error Model in Bioconductor
... The closest thing to the two component error model you're referring to (I think) is the Rocke, Durbin model (Bioinformatics, 2003, 19, 966-972). The last time I checked, there was code on David Rocke's web site. I think I've seen an R package there as well. Otherwise, still within the microarray fr ...
written 12.0 years ago by Greg Finak50
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Answer: A: Low Ratio values in LIMMA
... Hi, Nataliya. This is very much dependent on how you normalize your data. It's possible to "over normalize" and wipe out most of the variability in your data. If you're certain that this isn't the case, then, no, Limma doesn't generate shrunken estimates of the expression ratios, only t-statistics. ...
written 12.0 years ago by Greg Finak50

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