if the design matrix is constant then there are all sorts of way to speed things up. Using apply is probably the worst thing you could do... have a look at GSEAlm for some ways to compute fits, residuals and other diagnostics quickly. best wishes Robert Kasper Daniel Hansen wrote: > Use limma, as you are supposedly fitting the same model to every row. > > Kaspr > > On Apr 7, 2009, at 8:12 , Zheng, Xin (NIH) [C] wrote: > >> Hi there, >> >> I was doing anova on an array file. I know Partek can do it in >> minutes, yet it cost half an hour in R with apply(matrix, 1, function >> of anova). Any hint? Thanks. >> >> Xin Zheng >> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org