Hello,

I am trying to evaluate the association between a continuous predictor variable and array data using limma's lmFit.  I used the methyLumi package to create an eset to manage the data from the Illumina Infinium DNA methylation platform.  I am able to run a model if my exposure/predictor variable is categorical but when it is continuous I get an error.  I am wondering whether lmFit must be run with categorical predictor variables only.  If so, do you recommend something else to evaluate continuous predictor variables?



#Using a continuous predictor variable:
dm1 <- model.matrix(~continuousVar, model.frame(~continuousVar,data=pData(mldat),na.action=NULL))

fit1 <- lmFit(exprs(mldat), dm1, na.action=na.exclude)
Error in qr.default(x) : NA/NaN/Inf in foreign function call (arg 1)


#Using a categorical predictor variable:
dm2 <- model.matrix(~ Sex2, model.frame(~Sex2,data=pData(mldat), na.action=NULL))

fit2 <- lmFit(exprs(mldat), dm2, na.action=na.exclude)
#no error

Thank you.
Bonnie Joubert

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