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New statistical algorithms for Monitoring Gene Expression on GeneChip® Probe Arrays

evaluate whether the mean of the replicates in one tissue was significantly different from the mean of the replicates in the other tissue. The results are shown in Figure 8.

Overall, the Comparison calls generated by MAS 4.0 and MAS 5.0 are highly similar. The No Change calls of both MAS 4.0 and MAS 5.0 peak at approximately 0.9, as we would expect. The Decrease calls (D) peak at 1 and the Increase calls (I) peak towards zero for both algorithms, while the lines follow each other very closely. The additional benefit of MAS 5.0 is that we now have p-values to assess statistical significance of the comparisons of every gene.

The next technical note will contain more results on Comparison calls and their performance in MAS 5.0, together with discussions of tunable parameters and confidence limits.

Conclusions

In conclusion, our extensive validation studies, some results from which are shown above, allow us to state with confidence the following:

– The new statistical algorithms in MAS 5.0 perform as robustly and precisely as the previous algorithms, while providing the additional value of statistical significance (p values) and confidence limits, thereby offering GeneChip® users the ability to evaluate the significance of their results.

– Negative expression values (signals) have been eliminated; only positive values are generated in MAS 5.0.


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