[BioC] Probe pairs location on chips // ANOVA

[julien.sylvestre@wotan.ens.fr]

Hi,

* Does anyone knows whether the probe pairs for a single probe set are distributed around the array on HgU95 human chips and on YgS98 yeast chips ? 
I heard affy recently decided to separate them in order to "average" spacial effects but in the case of yeast chips looking at the images makes me thinks that it has not yet been done. Affy package Image 
methods for watching a definite probe set would probably haveto be adapted to take into account that new randomized chip design.

* As for the ANOVA problem I mentionned earlier, I had good results on calculating gene per gene effects and pairwise interactions using SAS and proc glm, which proved quite quickly and had no memory 
problems while R lm (and matlab anovan) both had. A solution could however certainly have been written in R.

Thanks.

JS.