BMC Genomics 2006, 7:252 http://www.biomedcentral.com/1471-2164/7/252 IFnitgeunrsiety6profiles of probesets with top 100 most deviant expression ratios following TwoRA Intensity profiles of probesets with top 100 most deviant expression ratios following TwoRA. The profiles are classified into four categories: A&C, the intensity is reduced in the tissue sample where the gene is more expressed (DRG, SN respectively). B&D, the intensity is increased in the sample where the gene is less expressed (SN, DRG respectively). Solid lines mark the shift in intensity from OneRA to TwoRA for one tissue sample. Dashed lines link the intensity data for equivalent probesets in the two biological samples. In colour are probesets with absent call 'A' in the SN (red) and DRG (blue). whole set of targets on the chip, we undertook an alterna- tive analysis. We selected all probesets where a shift in intensity following TwoRA in one sample would cause the intensity in the other sample to fall outside the intensity range, that is below the background noise or higher than the saturation level. These limits were chosen to be the 3% and 98% quantiles of the distribution of signal intensity on the chip, respectively. The analysis was conducted by first determining the maximum Δlog2IN (log2 TwoRA – log2 OneRA) across the two samples for each gene. Thus, if the maximum Δlog2IN is found in sample A, we add the same Δlog2IN to the OneRA log 2 intensity from sample B. If the resulting value is outside the chosen limits, the probeset is selected by our analysis. Page 9 of 14 (page number not for citation purposes)