Appendix 1. Expression Report Files

The full Affymetrix expression reports are presented in this appendix, for the six chips: D407-1, D407-2, D407-3, ARPE-1, ARPE-2 and ARPE-3. These reports describe a series of measures related to the quality of target hybridization and target preparation. Several factors are worth specific attention. The scaling factor relates to the degree of hybridization; in the present study this ranges from 3.5 to 6.7 (an acceptable range). The number present call reflects the overall quality of each experiment; in the present study this ranges from 37.7 to 44.8, which is very consistent between experiments. The quality of the targets is reflected in the 3' to 5' ratio of housekeeping genes. For example, GAPDH (probe set HUMGAPDH/M33197) has a 3' to 5' ratio that ranges from a low of 0.8 to a high of 1.9. This indicates that the amount of 3' end of the target is very similar to the amount of 5' end of the target. All of these measures provide the investigator the quality controls necessary to evaluate individual microarray experiments.

To access this data, click or select the words "Expression Report Files". This will initiate the download of a compressed (zip) archive. This file should be uncompressed with an appropriate program (the particular program will depend on your operating system). Once extracted, you will have a folder (or directory) containing six files (one for each microarray). The files are tab delimited text. Most spreadsheet and word processing programs will import files in this format.