Hello, Is there a way to easily filter genes on the average signal over groups (according to phenoData?). Let's say that in phenoData of my eset object I have 'Time' and 'Status' variables, which have 3 values each. I have 3 arrays for each of the (9) conditions. What I want is to keep genes with an average value of at least 100 in at least one of the resulting 9 conditions. The genefilter package seemingly only include functions to filter genes ignoring groups - is there an easy way to do the same taking into account groups? Thanks, Michael

Michael it is not difficult to write such a function, using "split" on your covariates, and then "lapply" and "rowMeans" on the resulting list of sets of arrays. The reason such a function does not exist in genefilter is that this type of filtering disturbs the null distribution of subsequently used t-statistics or F-statistics that are commonly used in per-gene hypothesis testing, and thus typically leads to invalid p-values. See the man page of the "nsFilter" (and the reference cited therein, which will appear soon). If you don't do hypothesis testing afterwards, i.e. if you use this filtering as a variable selection step e.g. for classification, clustering, then that is of course fine. Wolfgang Michael Imbeault scripsit 08/03/10 18:53: > Hello, > > Is there a way to easily filter genes on the average signal over groups > (according to phenoData?). Let's say that in phenoData of my eset object > I have 'Time' and 'Status' variables, which have 3 values each. I have 3 > arrays for each of the (9) conditions. > > What I want is to keep genes with an average value of at least 100 in at > least one of the resulting 9 conditions. The genefilter package > seemingly only include functions to filter genes ignoring groups - is > there an easy way to do the same taking into account groups? > > Thanks, > Michael > > _______________________________________________ > 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 -- Best wishes Wolfgang -- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber/contact