[BioC] tilingArray normalizeByReference Data Scaling

[Dario Strbenac]

Hello,

Could the description about what steps are done be made clearer ? Looking at the output, it seems that the data has been divided by the DNA values and log2 scaled after DNA reference normalisation. But there's no mention of this in ?normalizeByReference and the Bioinformatics article gives a number of different ways to normalise the data. I also notice that the 5% quantiles of the normalised results aren't scaled to 0. Is this an additional step ?

Looking at the source code, I also noticed that it log2 scales the reference probes and natural log scales the background probes. Is this intentional ?

Thanks,
       Dario.

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Dario Strbenac
Research Assistant
Cancer Epigenetics
Garvan Institute of Medical Research
Darlinghurst NSW 2010
Australia