[BioC] One-Color Agilent Data into Limma GUI

[J.delasHeras at ed.ac.uk]

Quoting elliot harrison <e.harrison at epistem.co.uk>:

> Hi Martin,
>
> Thanks for that.
> On your advice I remade the targets file from scratch and what do you
> know the data loaded.
>
>
> So I went back to the original post I was using as a guide
>
> 1. Use read.maimages() with dummy arguments for R & Rb
> Done
> 2. Background correct as usual using backgroundCorrect()
> Done
> 3. Normalize the RG$G matrix using normalizeBetweenArrays()
> Done
> 4. Use log2(RG$G) as input to lmFit() etc.
> Done
>
>
> They make no mention of normalising within arrays. Is this a bad idea
> with one colour data?

It's not a bad idea, it just cannot be done :-)
Normalisation within arrays aims to "balance" the two signals on a  
2-colour array. If you only have one colour... then you only normalise  
between samples/arrays.

Jose


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