I'd like to use the vsn package to normalize protein array data, as described in "Felgner et al 2009 PNAS 106:13499-13504 A burkholderia psuedomallei protein microarray reveals serodiagnostic and cross-reactive antigens". I have a set of "positive" and "negative" samples labelled with Cy3 and read in bluefuse, so I only have one "channel". I have read the "vsn" and "limma" documentation but the examples they give only seem to refer to two-color arrays and MA values. Can anyone suggest how I should progress?
 
Jabez
 
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