Reposting with new subject line as suggested And with more info as suggested design file and short gene file attached ======================= Am using maanova 1.14.0 Process runs to completion but ends with > ftest.Breed.mix_100perm090709F1FsRerun <- matest (BDeset_gcrma_WithAffyID090709, BGanova.Br_T.mix090709, term = "Breed", n.perm = 100, critical = .9, test.type = c("ftest"), shuffle.method = c("sample"), MME.method = c("REML"), test.method = c(1,1), pval.pool = TRUE, verbose = TRUE) Doing F-test on observed data ... Doing permutation. This may take a long time ... Finish permutation # 100 There were 50 or more warnings (use warnings() to see the first 50) > warnings() Warning messages: 1: In FUN(newX[, i], ...) : coercing argument of type 'double' to logical 2: In FUN(newX[, i], ...) : coercing argument of type 'double' to logical 3: In any(parsed.formula$random) : coercing argument of type 'double' to logical 4: In any(parsed.formula$random) : coercing argument of type 'double' to logical 5: In any(parsed.formula$random) : coercing argument of type 'double' to logical and on and on... the three commands are file2 <- read.madata("file1.txt", designfile="DesignV4LR081109.txt", header=TRUE, spotflag=FALSE, intensity=2, probeid=1) file3 <- fitmaanova(file2, formula=~Breed+Time, random= ~Time, covariate = ~1, verbose=TRUE) file4 <- matest (file2, file3, term = "Breed", n.perm = 1000, critical = .9, test.type = c("ftest"), shuffle.method = c("sample"), MME.method = c("REML"), test.method = c(1,1), pval.pool = TRUE, verbose = TRUE) > sessionInfo() R version 2.9.0 (2009-04-17) x86_64-apple-darwin9.6.0 locale: en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] maanova_1.14.0