[BioC] multtest Paired T-test error

[Ken Termiso]

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