

Hello All,

I am looking for a function or package in R / Bioconductor that can normalize single-colour cDNA arrays.

The experimental design contains three biological replicate chips for five time points (control and four points after treatment) and four treatment groups (strains of a given animal).  

The chip contains spiked-in controls at 5 orders of magnitude, and also housekeeping genes.

I've used vsn but it didn't seem to change the shape of the clouds.

Any pointers or advice would be appreciated - let me know if you need more details.

With kind thanks in advance,

Paul Lang
Oregon State University

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