Do you mean like in the following example? ## Create sample data set x <- matrix(rnorm(1000), 20, 5, dimnames=list(1:20, paste("t", 1:5, sep=""))) z <- data.frame(ID=paste("g", sort(rep(1:10, 2)), sep=""), x) myIDs <- unique(as.vector(z[,1])) ## Query A for rows rowQ <- z[rowSums(z[, -1]>=1)>=2, ] rowQ <- sort(unique(as.vector(rowQ[,1]))) ## Query B for columns colQ <- sapply(2:length(z[1,]), function(x) tapply(z[,x], z[,1], function(y) sum(y>=1))) colQ <- rowSums(colQ>=2) colQ <- sort(unique(as.vector(names(colQ[colQ>=1])))) ## Combine A & B with AND connection qID_AND <- intersect(rowQ, colQ) z[z[,1] %in% qID_AND, ] ## Combine A & B with OR connection qID_OR <- unique(c(rowQ, colQ)) z[z[,1] %in% qID_OR, ] Thomas On Sun 05/11/08 22:09, Dr Balazs Gyorffy wrote: > Thanks, but I think my description was somewhat loose. > > So: I have a table looking like this: > A B C D E > g1 1.51 0.96 0.70 0.34 1.38 > g1 0.69 1.22 0.73 0.62 0.74 > g2 0.35 0.14 0.83 1.58 0.49 > g2 0.20 0.61 0.53 0.24 0.06 > g3 0.00 0.69 1.79 0.84 0.42 > g3 0.96 0.77 1.28 0.32 0.82 > > so I have multiple probes per gene (up to 16, but here only 2). > > I am looking for the genes, in which at least TWO values in: > > A, one probe in two or more samples: e.g. A1:E1 > B, several probes in one sample: e.g. here A1:A2 > > are above the threshold. (e.g. here g1 and g3 meet the criteria if the > threshold is=1). > > And THEN I would like to extract all probes for the gene (e.g. here the result > table would include all g1 and all g3 probes). > > Thank you: > Balazs > > > --- Thomas Girke <thomas.girke at="" ucr.edu=""> schrieb: > > > Here is a simple example for finding all genes (rows) that have at least > > x instances of a given comparison per row (x here >=1). > > > > y <- matrix(rnorm(50), 10, 5, dimnames=list(paste("g", 1:10, sep=""), > > paste("t", 1:5, sep=""))) > > myQ <- y >= 1 > > myQcount <- rowSums(myQ) # counts TRUE values per row > > y[myQcount>=1,] > > > > I hope this helps. > > > > Thomas > > > > > > Nicht vergessen! Am Sonntag, den 11. Mai ist Muttertag > Geschenkideen, Gedichte & mehr: www.yahoo.de/muttertag > -- Thomas Girke Assistant Professor of Bioinformatics Director, IIGB Bioinformatic Facility Center for Plant Cell Biology (CEPCEB) Institute for Integrative Genome Biology (IIGB) Department of Botany and Plant Sciences 1008 Noel T. Keen Hall University of California Riverside, CA 92521 E-mail: thomas.girke at ucr.edu Website: http://faculty.ucr.edu/~tgirke Ph: 951-827-2469 Fax: 951-827-4437