Hi all,

I am trying to use the SNM package to normalize a dataset. The whole
dataset is a combination of Illumina arrays and Affymetrix arrays. I use
the batch effect to model the platform difference. Following is my code for
constructing the bio.var and adj.var matrices. The SNM function gives an
error of invalid model matrix. I noticed that on the SNM help page, it
highlights the necessity of making the model matrix valid. However, I am
not sure how to determine if the model matrices are valid. Could anybody
please help? Thank you very much.

Wendy

> Bio_var<-model.matrix(~groups,BioNames)   #65x12 matrix
> Adj_var<-model.matrix(~batches,Batch)  # 65x1 matrix
> snm.obj1<-snm(raw.data,bio.var=Bio_var,adj.var=Adj_var,int.var=NULL)
Error in make.snm.obj(Y = raw.dat, bio.var, adj.var, int.var, spline.dim,
 :
  cbind(bio.var,adj.var) is not a valid model matrix. Enter '?model.matrix'
for more information on building a model matrix.

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