[BioC] lmFit: Error in dimnames(fit$cov.coefficients)

[Mete Civelek]

Dear All,

I am getting an error when trying to do an analysis with the lmFit function
in the limma package. I can't get a handle at what the problem might be. I
will appreciate any insights you can provide. Thank you

Mete

library(limma)
memory.size(max = TRUE)
MData<-read.delim("MData.txt", header=T, row.names=1)
traits<-read.delim("MPheno.txt", header=T)
#gene expression in rows, samples in columns
dim(MData)
#43145 rows, 1396 samples
#samples in rows
dim(traits)
#301 traits and 1396 samples
ind<-match(names(MData), traits$MOMID)
traits<-traits[ind,]

for(j in 136:ncol(traits)){
form1 <- as.formula(paste(" ~ ",
paste(names(traits)[c(j,2:19)],collapse="+")))
design<-model.matrix(form1, data=traits)
#Determine the samples with NAs in traits
i <- !is.na(traits[,j])
rownames(design)<-colnames(METSIMData[,i])
fit<-lmFit(METSIMData[,i],design)
Error in dimnames(fit$cov.coefficients) <- list(coef.names[est],
coef.names[est]) :
  attempt to set an attribute on NULL

> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
States.1252    LC_MONETARY=English_United States.1252 LC_NUMERIC=C

[5] LC_TIME=English_United States.1252

attached base packages:
[1] parallel  splines   stats     graphics  grDevices utils     datasets
methods   base

other attached packages:
 [1] limma_3.16.8         scatterplot3d_0.3-33 WGCNA_1.27-1
doParallel_1.0.3     iterators_1.0.6      foreach_1.4.1        MASS_7.3-29

 [8] reshape_0.8.4        plyr_1.8             cluster_1.14.4
Hmisc_3.12-2         Formula_1.1-1        survival_2.37-4
flashClust_1.01-2
[15] dynamicTreeCut_1.60  impute_1.34.0

loaded via a namespace (and not attached):
[1] codetools_0.2-8 grid_3.0.1      lattice_0.20-23 rpart_4.1-3
tools_3.0.1


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