Quality control specifications for the second generation multi-species endocrine microarray.

Comparison of the performance characteristics of on both prototype (spotted oligonucleotide) and second generation (Agilent ink jet oligonucleotide) endocrine multi-species microarray platforms; Panels A and B: scatter plots of log₂ signal intensities of an individual fish from the Los Angeles Sanitation District versus the control fish pool. Panels A and B depict prototype and second generation platforms respectively. Panel C; direct comparison of platform sensitivity defined as log₂ ratio between treatment and ABC control. Panel D: Analysis of signal concordance. Panel E: Analysis of variance with both platforms. To measure internal consistency (variance of internal replicates), log₂ transformed expression value was plotted on the x-axis. Standard deviation is plotted on the y-axis, with a range of plus or minus one standard deviation from the mean expression value. The y-axis is a measure of the deviation of individual replicate probes stray from the mean value. The second generation platform has smaller variance of the internal replicates. Probe variance on both platforms is independent of the signal. Panel F: Comparison of the probe signal intensity distribution (plotted as log₂ transformed) for 149 probes that were present on both platforms.