On a Mac G5 with OSX 10.3 (updated) and R 2.0.1 I'm using multtest with good success until I tried to run a paired t-test...the other tests executed fine, but mt.teststat with test="pairt" didn't seem to like my class labels... m <- exprs(m579rma) m.cl <- c(0,0,0,1,1,1) # first 3 cols are control chips, last 3 cols are exp chips. m <- as.numeric(m) dim(m) <- c(22277,6) teststat_pairt_para_rma <- mt.teststat(m,m.cl,test="pairt",nonpara="n") 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 I then tried to see if it didn't like the zeroes in my classlabel... mpairedt.cl = c(1,1,1,2,2,2) teststat_pairt_para_rma <- mt.teststat(m,mpairedt.cl,test="pairt",nonpara="n") Error in mt.checkclasslabel(classlabel, test) : in paired t test, we only handle two groups your classlabel= 1 As per another message in the BioC archives entitled 'Bug Report: mt.teststat with test="pairt"', I rearranged my chips so that the order was con,exp,con,exp,con,exp instead of con,con,con,exp,exp,exp..."m_pairt" is the name of this rearranged matrix of my chips... m_pairt.cl <- c(1,2,1,2,1,2) teststat_pairt_para_rma <- mt.teststat(m_pairt,m_pairt.cl,test="pairt",nonpara="n") Error in mt.checkclasslabel(classlabel, test) : in paired t test, we only handle two groups your classlabel= 1 Should I just take the square root of the F-stat P-values to get the P-values for the paired t-test, or is there a workaround? Thanks in advance, Ken

Ken, For a "pairt" test, you need the labels to be 0's and 1's *and* to be ordered with pairs next to each other. So, this should work: labels<-c(0,1,0,1,0,1) stats<-mt.teststat(m,labels,test="pairt",nonpara="n") Also, be sure to reorder the columns of m accordingly. Best, Katie > ------------------------------ > > Message: 3 > Date: Thu, 27 Jan 2005 18:51:56 +0000 > From: "Ken Termiso" <jerk_alert@hotmail.com> > Subject: [BioC] multtest Paired T-test error > To: bioconductor@stat.math.ethz.ch > Message-ID: <bay101-f399a175aaec5f20717a3aee8780@phx.gbl> > Content-Type: text/plain; format=flowed > > On a Mac G5 with OSX 10.3 (updated) and R 2.0.1 I'm using multtest with good > success until I tried to run a paired t-test...the other tests executed > fine, but mt.teststat with test="pairt" didn't seem to like my class > labels... > > m <- exprs(m579rma) > m.cl <- c(0,0,0,1,1,1) # first 3 cols are control chips, last 3 cols are exp > chips. > m <- as.numeric(m) > dim(m) <- c(22277,6) > teststat_pairt_para_rma <- mt.teststat(m,m.cl,test="pairt",nonpara="n") > > 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 > > > > I then tried to see if it didn't like the zeroes in my classlabel... > > > > mpairedt.cl = c(1,1,1,2,2,2) > teststat_pairt_para_rma <- > mt.teststat(m,mpairedt.cl,test="pairt",nonpara="n") > > Error in mt.checkclasslabel(classlabel, test) : > in paired t test, we only handle two groups > your classlabel= 1 > > > > As per another message in the BioC archives entitled 'Bug Report: > mt.teststat with test="pairt"', I rearranged my chips so that the order was > con,exp,con,exp,con,exp instead of con,con,con,exp,exp,exp..."m_pairt" is > the name of this rearranged matrix of my chips... > > > > m_pairt.cl <- c(1,2,1,2,1,2) > teststat_pairt_para_rma <- > mt.teststat(m_pairt,m_pairt.cl,test="pairt",nonpara="n") > Error in mt.checkclasslabel(classlabel, test) : > in paired t test, we only handle two groups > your classlabel= 1 > > > > Should I just take the square root of the F-stat P-values to get the > P-values for the paired t-test, or is there a workaround? > > Thanks in advance, > Ken