2. Affymetrix Latin Square Experiment One lot of 14 arrays were used for the study using spikes along with the background-- enriched RNA from DR153 (Ecoli) strain. Twenty assay spikes were labeled transcripts generated from the deletion area of DR153 chromosome, while their background RNA was isolated from DR153, subsequently enriched and direct-labeled. The twenty assay spikes were grouped into 14 sets and its concentration (nM) prepared in the mix according to the Latin-square scheme.

3. Latin Square Scheme

4. Model for one probe set Full model Reduced model

5. Scanning Saturation Probe 1-15: PM and MM data overlaid. Probe 1-30: PM and MM data concatenated Probe 1-30: Red fitted curve overlaid.

11. Saturation

12. Histograms of cel intensities of the 14 arrays

13. Handle Saturation mean Observed value (saturation limit)

14. Conditional Expectation

15. Conditional Expectation (cont’d)

16. After imputing saturated data points Probe 1-15: PM and MM data overlaid. Probe 1-30: PM and MM data concatenated Probe 1-30: Red fitted curve overlaid.

22. PM only Model

23. MM only model

24. Reduced model

25. Reduced(black) vs AD(orange) square root

26. Full model without imputation

27. Full model with imputation

28. Full w/o (black) vs full w/ (red) Transformed to same scale

29. Full w/o (black) vs full w/ (red) same scale square root