[BioC] tilingArray normalizeByReference Data Scaling

Dario Strbenac d.strbenac at garvan.org.au
Tue May 15 04:00:22 CEST 2012

Thanks for the clarification. Yes, I was confused which one of the options in 
Figure 5 of the article were implemented in the tilingArray packages.

What I meant by the difference in log bases is :

refSig = rowMeans(log2(exprs(reference)[pm, , drop = FALSE]))
ybg[, j] = tapply(log(exprs(x)[background, j], 2), strata, genefilter::shorth, 
tie.action = "min")

?log says the default base is e. So is there a mathematical reason to use base 
2 for reference probes, and base e for background probes ?

- Dario.

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