> Is there any limit ratio of between-array weight values, which one > can get using the arrayWeights() function in the limma package > <http: www.biomedcentral.com="" 1471-2105="" 7="" 261="" abstract="">? For > instance, if one array has the weight value - let's say - 4 and the > rest between 0.5 and 1.5, shall I keep the array and use it with > the weight array, or rather discard the one array and apply again > the arrayWeights() again and continue to results? I am particularly > interested in answers related to the mouse 430_2 chips. > Regards, Radek > Radek Blatny, MSc. > Institute of Molecular Genetics > Department of Mouse Molecular Genetics (Jiri Forejt unit) > Czech Academy of Sciences > Videnska 1083 > 142 20, Prague > Czech Republic > Tel. (+420) 241 062 260 > Fax (+420) 241 062 154 > http://www.img.cas.cz/mmg > email: blatny at img.cas.cz > Skype name: blatny

Hi Radek, Arrays with weights less than 1 are less precise than average, while arrays with weights greater than 1 are more precise (the sum to zero constraint in the log-linear variance model enforces this). So in your example, the array which is assigned a weight of 4 is the most precise array in the experiment, therefore I wouldn't recommend tossing it out. The idea behind the array weighting method is to keep all of the arrays in your analysis and weight the observations in the gene-wise linear models by the estimated array weights which are intended to account for differences in precision between different arrays. I hope this explanation helps. Best wishes, Matt >> Is there any limit ratio of between-array weight values, which one >> can get using the arrayWeights() function in the limma package >> <http: www.biomedcentral.com="" 1471-2105="" 7="" 261="" abstract="">? For >> instance, if one array has the weight value - let's say - 4 and the >> rest between 0.5 and 1.5, shall I keep the array and use it with >> the weight array, or rather discard the one array and apply again >> the arrayWeights() again and continue to results? I am particularly >> interested in answers related to the mouse 430_2 chips. > >> Regards, Radek > >> Radek Blatny, MSc. >> Institute of Molecular Genetics >> Department of Mouse Molecular Genetics (Jiri Forejt unit) >> Czech Academy of Sciences >> Videnska 1083 >> 142 20, Prague >> Czech Republic >> Tel. (+420) 241 062 260 >> Fax (+420) 241 062 154 >> http://www.img.cas.cz/mmg >> email: blatny at img.cas.cz >> Skype name: blatny