Hi all, I have a matrix of "A"/"P" calls. I want to filter for the probes that are present on all the replicates, for example sample1_1 sample1_2 sample2_1 sample2_2 gene1 A P P P gene2 P P A P gene3 A P A P gene4 A A A A ... I want to select for gene1 and gene2. I guess this a computational question. As I am new to R, could anybody give me some hints...Thank you in advance. Wendy [[alternative HTML version deleted]]

There are probably more elegant ways to do this but the following should work: ind <- which(apply(mat, 1, function(x) all(x[,1:2]=="P") | all(x[,3:4]=="P"))) filtered.mat <- mat[ind,] Matt On Fri, Apr 15, 2011 at 2:43 PM, Wendy Qiao <wendy2.qiao at="" gmail.com=""> wrote: > Hi all, > > I have a matrix of "A"/"P" calls. I want to filter for the probes that are > present on all the replicates, for example > ? ? ? ? ?sample1_1 ? ? ? sample1_2 ? ? ? ?sample2_1 ? ? ? sample2_2 > gene1 ? ? ?A ? ? ? ? ? ? ? ? ? P ? ? ? ? ? ? ? ? ? ? ? P ? ? ? ? ? ? ? ? ?P > gene2 ? ? ?P ? ? ? ? ? ? ? ? ? P ? ? ? ? ? ? ? ? ? ? ?A ? ? ? ? ? ? ? ? ? P > gene3 ? ? A ? ? ? ? ? ? ? ? ? P ? ? ? ? ? ? ? ? ? ? ?A ? ? ? ? ? ? ? ? ? ?P > gene4 ? ? A ? ? ? ? ? ? ? ? ? A ? ? ? ? ? ? ? ? ? ? A > A > ... > > I want to select for gene1 and gene2. I guess this a computational question. > As I am new to R, could anybody give me some hints...Thank you in advance. > > Wendy > > ? ? ? ?[[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Matthew N McCall, PhD 112 Arvine Heights Rochester, NY 14611 Cell: 202-222-5880