Hi, I have a microarray matrix 3000x70 for example (genes x experiments). This data has more than 2 classes. I would like to make some filtering on the genes. For example, I would like to exclude genes with the same mean expression across all classes. This is a problem of ANOVA H0:mu1=mu2=...=muk H1: at least one is different First question: Do you think Anova is reasonable for this? Second question. How can I do this with R? Clearly, I'll have to make some loop to apply this operation to all the genes. Thanks Luis -- A nossa prenda de Natal: Kit SAPO.ADSL.PT agora a 0 ? e Tr?fego Ilimitado. S? at? 31 de Dezembro. Adira j? em http://www.sapo.pt/kitadslgratis
Anova
2 messages · Luis Silva, Ramon Diaz-Uriarte
Dear Luis, You might want to take a look at the multtest and genefilter packages (which are part of Bioconductor ---www.bioconductor.org---; links to it also from R's web page). Note, however, that no explicit loop would be necessary anyway, since you can use, say, apply(my.data, 1, my.anova.function) asuming your data are in a data frame "my.data", where genes are in rows, and your "my.anova.function" returns whichever component from an aov or summary(aov) you are interested in. Hope this helps. Ram?n
On Thursday 12 December 2002 19:45, Luis Silva wrote:
Hi, I have a microarray matrix 3000x70 for example (genes x experiments). This data has more than 2 classes. I would like to make some filtering on the genes. For example, I would like to exclude genes with the same mean expression across all classes. This is a problem of ANOVA H0:mu1=mu2=...=muk H1: at least one is different First question: Do you think Anova is reasonable for this? Second question. How can I do this with R? Clearly, I'll have to make some loop to apply this operation to all the genes. Thanks Luis
Ram?n D?az-Uriarte Bioinformatics Unit Centro Nacional de Investigaciones Oncol?gicas (CNIO) (Spanish National Cancer Center) Melchor Fern?ndez Almagro, 3 28029 Madrid (Spain) http://bioinfo.cnio.es/~rdiaz