There are a few updates on June 3, 2005:
You can subtract a baseline if there are multiple measurements on same individual.
Each chip can be permanently omitted from all analyses.
For One Factor ANOVA, either raw data or log transformed data can be used.
Starting from Apr. 21, 2005, both One Factor ANOVA and Multi Factor ANOVA use log transformed signal values
for calculation.
Starting from Dec.17, 2004, FDR calculation is based on the number of genes after filtering by
Fraction Present filter instead of the total number of genes on the chip.