Used RMA (in Biocondutor package) to normalize these data. Completed 1/25/06.
Need to save the local class results so that we can look at specific differences (e.g., we need to examine the specific pair-wise comparisons). Question: Can SAFE do this? Does it perform a permutation ANOVA? If not, we will need to look at the following 2-sample tests: control versus day 1 and control versus day 3.
After 2/1/06 meeting it was decided to approach this analysis in two phases. The first will be the examination of probe level (local) analyses:
this will be compared to analysis based on SAFE analysis (both local and global) -- here we may need to make sure we have the directional information for each pairwise difference, so we can compare.
Prior analysis done by microarray core (normalized using MAS?) with the criteria of day 1 > control AND day 3 > 0 generated a final list of 466 probes (from 7,187). When the SAFE list is generated we will rank the products of p-values for the pairwise differences (multiply the p-values for each comparison) and plot the ranks (analysis 1 versus SAFE) to see what type of correspondence there is between these analyses. Additionally, we will generate a Venn diagram of the overlapping genes.