[BioC] How to import the original data into knncat?

Liu, Xin Xin.Liu at arragen.com
Tue Jun 15 16:53:53 CEST 2004

Dear all,

The following example in the package of knncat run well in R, so we hope to cluster our data just following this. The problem is how to import the data, how to build the vector and matrix? The first collumn should be the indentifier? the second collumn should be the expression average? and the third collumn should be the classifier? The data should be imported as a text file, Excel file or other type of file? Any clue? Thanks a lot!

library(MASS) # Load data set
syncat <- knncat (synth.tr, classcol=3)
## Not run: 
Train set misclass rate: 16.8
synpred <- predict (syncat, synth.tr, synth.te, train.classcol=3,
table (synpred, synth.te$yc)
synpred 0   1  
      0 466  61
      1  34 439
# Or do the whole thing in one pass:
## End(Not run)
knncat (synth.tr, synth.te, classcol=3)
## Not run: 
Test set misclass rate: 9.5
## End(Not run)


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