Figure 2

Signal normalization amongst tissues and resultant clustering. A box plot representation of signal normalization is presented in panel A. All nectary and non-nectary reference tissue hybridization files (.cel) were quality inspected and then normalized together using the Expressionist^® (Genedata, Basel, Switzerland) Refiner module in order to compare gene expression between nectaries and non-nectary tissues. Briefly, .cel files were loaded into Refiner, analyzed and inspected for defective area, average intensity, corner noise, and housekeeping control genes. The probe signals on each .cel file then were quantile normalized and summarized into probe set intensity values by applying the Robust Multiarray Average (RMA) algorithm [69]. Following normalization, signal ratio comparisons between nectaries and reference tissues identified large numbers of genes preferentially expressed within nectaries (panel B), which are presented in Additional file 7.