ysis was performed using the Affymetrix platform- specific software (present calls, signal intensity values) and MS Excel for calculation of the correlation factors (r2).

Data Analysis
We first analyzed the present call percentage. The number of present calls equals the number of genes (probe sets) that are detectable on a chip. This number corresponds to the genes being expressed in the particular sample.



A significant increase in the number of present calls was observed for both samples when labeled targets were prepared with the RAS Microarray Kits as shown in Table 1.



Figure 2 shows the distribution of the present calls in more detail. The genes analyzed are those that were detected with all three target replicates, prepared by the indicated workflow. For sample 1, 10,339 genes were found to be present when targets were prepared with the RAS Microarray Kits. Of these, 9,331 were also detected with all three targets prepared by Supplier As workflow.



For sample 2, when targets were prepared with the RAS Microarray Kits, 9,652 genes were detected. 7,887 of these genes were also detected with all three targets when Supplier As workflow had been used.

Using the RAS Microarray Kit workflow for target preparation, we identified 185 genes for sample 1 and 283 genes for sample 2 that could not be detected with any replicate when targets where prepared by Supplier As workflow. Vice versa, only 63 genes for sample 1 and 21 genes for sample 2 were not detected with targets prepared with the RAS Microarray Kits


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