What it probably means is that you can't make a silk purse out of a sow's ear: all those missings in your your data do not allow you to estimate the model(s) that you've specified.
If you don't know what this means, I suggest you seek the help of a local statistician. -- Bert Gunter Genentech -----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Leonardo Sent: Monday, January 14, 2008 8:51 AM To: r-help@r-project.org Subject: [R] Error in solve.default message using lme Dear All, Im using lme to analyze a time series gene expression data. I dont have all animals in all times, the number of animals in each time is different and I have lots of NA values. An example file can be downloaded at lbmp.fcav.unesp.br/leonardo and the code used is the following: teste<-read.table(file='example.csv',sep=',',header=T) B<-1366 library(nlme) pValueTime<-matrix(nrow=B,ncol=2) colnames(pValueTime)<-c('geneID','pValue.Time') for (i in 1:B) { print(i) gene = teste$gene [i] keep<-teste$gene==gene MTemp =as.numeric( teste$M [keep]) timeTemp = as.factor(teste$time [keep]) animalTemp = as.factor(teste$animal [keep]) tempMM.HA<-lme(MTemp~timeTemp,random=~1|animalTemp,method='ML', na.action=na.omit) tempMM.H0<-lme(MTemp~1,random=~1|animalTemp,method='ML', na.action=na.omit) pValueTime[i,1]<-gene pValueTime[i,2]<-anova(tempMM.HA,tempMM.H0)[2,9] } Im getting the following error message: Error in solve.default(estimates[dimE[1] - (p:1), dimE[2] - (p:1), drop = FALSE]) : system is computationally singular: reciprocal condition number = 1.64483e-17 I dont know what this message means, so any help/suggestion will be very appreciated. sessionInfo() R version 2.6.0 (2007-10-03) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] nlme_3.1-86 loaded via a namespace (and not attached): [1] grid_2.6.0 lattice_0.17-2 tools_2.6.0 Best regards, Leonardo ____________________________________ MSc. Leonardo Bernardes da Rocha Doctorate Student - Animal Science Department of Tecnology College of Agricultural and Veterinary Sciences São Paulo State University Jaboticabal, SP - Brazil Phone: +55 16 32092675 (Ext. 206) Email: [EMAIL PROTECTED] ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.