I am trying to correct for the effect of 2 covariates in a gene expression data set.


design<-model.matrix(~0 + Factor + cov1 + cov2)


QUESTION:
How to set up the contrast matrix?

The usual commands

fit <- lmFit(selDataMatrix, design)
cont.matrix <- makeContrasts(FacCont=Group1-Group2, levels=design)
fit2 <- contrasts.fit(fit, cont.matrix)

gives an error message because the original design matrix includes the covariates.

Error in contrasts.fit(fit, contrast.matrix) :
  Number of rows of contrast matrix must match number of coefficients
  In addition: Warning messages:
1: In rn != cn :
  longer object length is not a multiple of shorter object length
2: In contrasts.fit(fit, contrast.matrix) :
  row names of contrasts don't match col names of coefficients



I think I don't really understand how the contrast matrix works.


John W. Belmont, M.D.,Ph.D.
Professor
Department of Molecular and Human Genetics
Baylor College of Medicine
1100 Bates, Room 8070
Houston, TX 77030
713-798-4634
fax: 713-798-7187




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