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 [[alternative HTML version deleted]]

Sep/26/11 4:49 PM, Jabez Wilson scripsit:: > 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? > Dear Jabez have a look at section 3 of the vsn vignette (Running VSN on data from multiple arrays - single colour normalisation) Best wishes Wolfgang Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber