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.

On Tue, 7 May 2002 julien.sylvestre@wotan.ens.fr wrote: > 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. I'm fairly certain the HgU95 are, don't know about the yeast chips (the drosophilia chips are randomly distributed). > > * 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. > > Byron Ellis (bellis@hsph.harvard.edu) "Oook" - The Librarian Please finger bellis@hsph.harvard.edu for PGP keys > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >

On Tue, May 07, 2002 at 11:52:32AM +0200, julien.sylvestre@wotan.ens.fr wrote: > 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 ? Try help(plotLocation) to see how location of PPSet can be displayed over the 'image' of a chip. > 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. > The package is suited for wherever the probes for PPSet are located. > * 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. > i Fitting model per gene can be done at no memory cost in R (look again at filtertheniter in genefilter... if you still cannot see I can give hints (after my lunch break)) Hopin' it helps, Laurent -------------------------------------------------------------- Laurent Gautier CBS, Building 208, DTU PhD. Student D-2800 Lyngby,Denmark tel: +45 45 25 24 85 http://www.cbs.dtu.dk/laurent