I want to filter my expression data to accept only genes that have the MAS5 "present" call in at least 2 out of 5 samples. How could I do that? I know there are ALL and ANY commands in R, is there something like a SOME or AT_LEAST command? Thanks Andreas -- PLEASE NOTE MY NEW EMAIL ADDRESS: ANDREAS.ZANKL at GMAIL.COM -------------------------- Andreas Zankl, MD Division of Molecular Pediatrics Clinique Infantile 02/50 CHUV Avenue Pierre Decker 2 CH-1011 Lausanne Switzerland Phone: +41-21-3143778 Fax: +41-21-3143546 Email: andreas.zankl at gmail.com

Andreas Zankl wrote: > I want to filter my expression data to accept only genes that have > the MAS5 "present" call in at least 2 out of 5 samples. How could I > do that? I know there are ALL and ANY commands in R, is there > something like a SOME or AT_LEAST command? Easy enough to do without such a function. Say you have all the present/absent calls in a matrix called 'pcalls'. index.calls <- pcalls == "Present" index <- rowMeans(index.calls) =< 2 > > Thanks > Andreas > -- James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623

Hi, Have a look at the pairwise.comparison and pairwise.filter methods in simpleaffy. Alternatively, you could try something like (assuming x contains your matrix of PMA calls): x[x=="P"] <- 1 x[x!=1] <- 0 sums <- apply(x,1,sum) keep <- (sums >= 2) crispin -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Andreas Zankl Sent: 13 October 2005 16:01 To: bioconductor at stat.math.ethz.ch Subject: [BioC] how to select on Present calls in 2 out of 5 chips I want to filter my expression data to accept only genes that have the MAS5 "present" call in at least 2 out of 5 samples. How could I do that? I know there are ALL and ANY commands in R, is there something like a SOME or AT_LEAST command? Thanks Andreas -- PLEASE NOTE MY NEW EMAIL ADDRESS: ANDREAS.ZANKL at GMAIL.COM -------------------------- Andreas Zankl, MD Division of Molecular Pediatrics Clinique Infantile 02/50 CHUV Avenue Pierre Decker 2 CH-1011 Lausanne Switzerland Phone: +41-21-3143778 Fax: +41-21-3143546 Email: andreas.zankl at gmail.com _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor -------------------------------------------------------- This email is confidential and intended solely for the use o...{{dropped}}

Or alternatively you can use rowSums (assuming x contains your matrix of PMA calls): calls.sum <- rowSums(x=="P") keep <- names(calls.sum[calls.sum>=2]) It's a little faster! claire -- Claire Wilson Bioinformatics Group Paterson Institute for Cancer Research Christie Hospital NHS Trust Wilmslow Road Manchester M20 4BX tel: +44 (0)161 446 8218 url: http://bioinf.picr.man.ac.uk/bioinf/cwilson.jsp -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Crispin Miller Sent: 13 October 2005 16:59 To: Andreas Zankl Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] how to select on Present calls in 2 out of 5 chips Hi, Have a look at the pairwise.comparison and pairwise.filter methods in simpleaffy. Alternatively, you could try something like (assuming x contains your matrix of PMA calls): x[x=="P"] <- 1 x[x!=1] <- 0 sums <- apply(x,1,sum) keep <- (sums >= 2) crispin -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Andreas Zankl Sent: 13 October 2005 16:01 To: bioconductor at stat.math.ethz.ch Subject: [BioC] how to select on Present calls in 2 out of 5 chips I want to filter my expression data to accept only genes that have the MAS5 "present" call in at least 2 out of 5 samples. How could I do that? I know there are ALL and ANY commands in R, is there something like a SOME or AT_LEAST command? Thanks Andreas -- PLEASE NOTE MY NEW EMAIL ADDRESS: ANDREAS.ZANKL at GMAIL.COM -------------------------- Andreas Zankl, MD Division of Molecular Pediatrics Clinique Infantile 02/50 CHUV Avenue Pierre Decker 2 CH-1011 Lausanne Switzerland Phone: +41-21-3143778 Fax: +41-21-3143546 Email: andreas.zankl at gmail.com _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor -------------------------------------------------------- This email is confidential and intended solely for the use\ ...{{dropped}}