[BioC] limma Within Array Normalisation By Controls

[Dario Strbenac]

Hello,

I have an experiment where there are some Nimblegen 2.1 million probe Mouse promoter arrays with IPs always in the red channel and input DNA always in the green channel. I notice that the arrays have some probes of type Random, which I assume should not be changing between channels. So, I'd like to use normalizeWithinArrays with method = "control". I call the method as :

normalizeWithinArrays(RG, method = "control", controlspots = RG$genes$Status == "Random")

and get the error :

Error in normalizeWithinArrays(RG, method = "control", controlspots = RG$genes$Status ==  : 
  Layout argument not specified

I'm confused as to why it requires the layout ? I didn't think newer array designs had print tip groups or replicate spots ?

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