Hi I am having problems with multtest and it is really annoying because I know I am being stupid! I read a tab-delimited text file in using read.table, into a variable called "data". data has 12 columns, 1-5 being annotation and 6-12 (7 columns) being actual data. When I try: > t <- mt.teststat(data[,6-12], c(0,0,0,1,1,1,1), test="t") I get errors: Error in mt.checkX(X, classlabel, test) : the number of column of X needs to be the same as the lengtho of classlabel your X= 1 your classlabel is 0 I just know I am being ridiculously stupid and it's probably that I don't remember how to use R properly, but can someone tell me how to use mt.teststat with data read in from a text file using read.table? Thanks Mick

Hi all, Whats the easiest way to read published data in the SMD database into R. The "raw data" from smd.stanford.edu seems to download as multiple excel files, which fail to be read into R if I use read.SMD(). Am I downloading the incorrect format file from SMD? Thanks so much for any help, Aedin

Its a typo Try (6:12) instead of (6-12) e.g. > t <- mt.teststat(data[,6:12], c(0,0,0,1,1,1,1), test="t") -----Original Message----- From: michael watson (IAH-C) To: bioconductor@stat.math.ethz.ch Sent: 24/02/04 13:32 Subject: [BioC] problems with multtest Hi I am having problems with multtest and it is really annoying because I know I am being stupid! I read a tab-delimited text file in using read.table, into a variable called "data". data has 12 columns, 1-5 being annotation and 6-12 (7 columns) being actual data. When I try: > t <- mt.teststat(data[,6-12], c(0,0,0,1,1,1,1), test="t") I get errors: Error in mt.checkX(X, classlabel, test) : the number of column of X needs to be the same as the lengtho of classlabel your X= 1 your classlabel is 0 I just know I am being ridiculously stupid and it's probably that I don't remember how to use R properly, but can someone tell me how to use mt.teststat with data read in from a text file using read.table? Thanks Mick _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor ********************************************************************** This email and any files transmitted with it are confidentia...{{dropped}}

Hi Michael, > > t <- mt.teststat(data[,6-12], c(0,0,0,1,1,1,1), test="t") Try > t <- mt.teststat(data[,6:12], c(0,0,0,1,1,1,1), test="t") ^^^^^ Regards, Marcel -- _____________________________________________________________ Marcel Dettling ETH Z?rich Seminar f?r Statistik LEO C 12.2 8092 Z?rich Phone: ++41 1 632 53 19 E-Mail: dettling@stat.math.ethz.ch Web: http://stat.ethz.ch/~dettling/

I believe your problem is in the call to mt.teststat. You want to subset your data using a colon rather than an hyphen (data[,6:12] rather than data[,6-12]). Best, Jim 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 >>> "michael watson (IAH-C)" <michael.watson@bbsrc.ac.uk> 02/24/04 08:32AM >>> Hi I am having problems with multtest and it is really annoying because I know I am being stupid! I read a tab-delimited text file in using read.table, into a variable called "data". data has 12 columns, 1-5 being annotation and 6-12 (7 columns) being actual data. When I try: > t <- mt.teststat(data[,6-12], c(0,0,0,1,1,1,1), test="t") I get errors: Error in mt.checkX(X, classlabel, test) : the number of column of X needs to be the same as the lengtho of classlabel your X= 1 your classlabel is 0 I just know I am being ridiculously stupid and it's probably that I don't remember how to use R properly, but can someone tell me how to use mt.teststat with data read in from a text file using read.table? Thanks Mick _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor