[BioC] limma and single-dye (R) gpr

[Paul Geeleher]

Check out this previous thread from the mailing list:

http://article.gmane.org/gmane.science.biology.informatics.conductor/18032
/match=read+single+channel+genepix+limma+analyze+miRNA+experiment

There are other previous threads that you will find useful too if you
try searching the mailing list:

http://dir.gmane.org/gmane.science.biology.informatics.conductor

-Paul


On Mon, Jun 2, 2008 at 11:25 AM, Ng Stanley <stanleyngkl at gmail.com> wrote:
> Hi,
>
> I have inherited a set of single-dye (R) gpr, and need to process them via
> limma. After several tries, managed to load via read.maimages and
> backgroundCorrect using dummies values for G and Gb from R and Rb,
> respectively. Two questions:
>
> A) Am I right to say that normalizeWithinArrays for single-dye gpr ?
> B) How to normalize between arrays in the right way ? Should it
> be normalizeBetweenArrays(RG, method="quantile")  or
> normalizeBetweenArrays(RG$R, method="quantile") or something else ?
>
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