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Hi, I think you could try to average your replicates and after that perform the paired test. hth Manuel --- Ozge Gursoy-Yuzugulu <sehriban at="" bilkent.edu.tr=""> escribi?: > hi, > > I am using "multtest" to analyze my data. Data > consisit of 2 groups > with 3 different conditions in each with 2 > repllicates. I encounter > with the following error. > > n = read.csv("G2vs2215minus.csv") > > dim(n) > [1] 54675 13 > > m = n[,2:13] > > nlabel = c(0,0,1,1,0,0,1,1,0,0,1,1) > > tmp <- mt.teststat.num.denum(m, nlabel, test = > "pairt") > Error in mt.checkclasslabel(classlabel, test) : > Some errors in specifying classlabel for the paired > t test > for the block 1 located at ( 1 2 ) > your classlabel= 0 > Some errors in specifying classlabel for the paired > t test for the > block 1 located at ( 1 2 ) > your classlabel= 0 > Some errors in specifying classlabel for the paired > t test for the > block 1 located at ( 1 2 ) > your classlabel= 1 > Some errors in specifying classlabel for the paired > t test for the > block 1 located at ( 1 2 ) > your classlabel= 1 > Some errors in specifying classlabel for the paired > t test for the > block 1 located at ( 1 2 ) > your classlabel= 0 > Some errors in specifying classlabel for the paired > t test for the > block 1 located at ( 1 2 ) > your classlabel= 0 > Some errors in specifying classlabel for the paired > t test for the > block 1 located at ( 1 2 ) > your classlabel= 1 > Some errors in specifying classlabel for the paired > t test for the > block 1 located at ( 1 2 ) > your classlabel= 1 > Some errors in specifying cla > > what should I do, to do a pair T test with 2 > replicates of data. > > > thank you all > [[alternative HTML version deleted]] > > _______________________________________________ > 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 >

Dear Ozge, > I am using "multtest" to analyze my data. Data consisit of 2 groups > with 3 different conditions in each with 2 repllicates. I encounter > with the following error. > > n = read.csv("G2vs2215minus.csv") > dim(n) > [1] 54675 13 > m = n[,2:13] > nlabel = c(0,0,1,1,0,0,1,1,0,0,1,1) > tmp <- mt.teststat.num.denum(m, nlabel, test = "pairt") > Some errors in specifying classlabel for the paired t test for the > block 1 located at ( 1 2 ) > your classlabel= 1 > Some errors in specifying cla > > what should I do, to do a pair T test with 2 replicates of data. If you change nlabel to nlabel = c(0,1,0,1,0,1,0,1,0,1,0,1) and rearrange your columns in the data frame m accordingly everything should work. multtest requires the paired data columns to be adjacent. Regards Gerhard ---------------------------------------------------------------------- -- DI Gerhard Thallinger E-mail: Gerhard.Thallinger at tugraz.at Institute for Genomics and Bioinformatics Web: http://genome.tugraz.at Graz University of Technology Tel: +43 316 873 5343 Petersgasse 14/V Fax: +43 316 873 5340 8010 Graz, Austria Map: http://genome.tugraz.at/Loc.html