Hi All! I have a table. Rows: genes - one gene is represented by several probes, colums: samples. Values: expression ratios. I would like to get the values for all samples and all probes for those genes, which have an expression ratio higher that 2 in at least 2 different measurements. (Thus these "measurements" can represent values of A, one probe in two or more samples or B, several probes in one sample, or C, any combination of these.) How can I make this? Thanks Balazs ------------------------- Bal?zs GY?RFFY MD, PhD Children's Hospital Boston Informatics Program Harvard-MIT Health Sciences and Technology 300 Longwood Avenue, Boston, USA Enders 150.6 Tel: +1 617 919 2654 Email: zsalab2 at yahoo.com Nicht vergessen! Am Sonntag, den 11. Mai ist Muttertag Geschenkideen, Gedichte & mehr: www.yahoo.de/muttertag

You may want to get familiar with basic R comparisons applied to matrices (or data frames), and how to add up the logical results with functions like rowSums(). The rest is standard subsetting of R objects with logical vectors. 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 On Sun 05/11/08 15:23, Dr Balazs Gyorffy wrote: > Hi All! > > I have a table. Rows: genes - one gene is represented by several probes, > colums: samples. Values: expression ratios. > > I would like to get the values for all samples and all probes for those genes, > which have an expression ratio higher that 2 in at least 2 different > measurements. > > (Thus these "measurements" can represent values of A, one probe in two or more > samples or B, several probes in one sample, or C, any combination of these.) > > How can I make this? > > Thanks > Balazs > > > ------------------------- > Bal?zs GY?RFFY MD, PhD > Children's Hospital Boston Informatics Program > Harvard-MIT Health Sciences and Technology > 300 Longwood Avenue, Boston, USA > Enders 150.6 > Tel: +1 617 919 2654 > Email: zsalab2 at yahoo.com > > > Nicht vergessen! Am Sonntag, den 11. Mai ist Muttertag > Geschenkideen, Gedichte & mehr: www.yahoo.de/muttertag > > _______________________________________________ > 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 > -- 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