Figure 9

Present/absent calls for each PCR pool. Influence of plate amplification on presence detection and probe brightness. The hybridized cRNA is made of clone pools of given concentrations, and each such pool is made from clones amplified from different plates. The plate numbers are given on the horizontal axis, while the nominal pool concentration is indicated by the color. The top two figures show the false negative ratio (that is, the proportion of probesets falsely called absent) for (a) C and (b) S samples, as all probesets that can be mapped to a clone should be called present. (c,d) The average PM probe intensity of clean probes prior to any normalization or NSB correction. Clean probes match perfectly their target sequence with little promiscuity from other clones' sequences. The figure shows important variations in the amplification efficiency from one plate to the next. The plots show that the proportion of false negatives is highly inversely correlated to the average probe intensity and identifies two 'failed' labeling reactions (plate 17 of concentration 0.27 μg pool, plate 6 of concentration 0.37 μg pool).