The database contains multiple matrixes that can be analyzed;
all genes quintile
metabolic genes quintile
all genes presentCall
metabolic genes presentCall
“all genes” vs. “metabolic”
The search can target all the genes in the database (“all genes”), or can be restricted to metabolic genes (“metabolic genes”). If the gene of interest is a metabolic gene, limiting the search to the “metabolic genes” option will yield faster results (see Note).
Quantile normalization matches up the individual array distribution across all arrays, so that the largest and the smallest of each distribution are equal (default).
Affymetrix results can be analyzed to determine whether a given gene is expressed or not. If a gene is determined not to be expressed in a given array, it will be assigned the relative expression value of 1. (The value 1 represents an extremely low relative expression.)
Since the “metabolic genes” matrix is smaller then the “all genes” matrix (1,704 vs. 17,788 genes) the computation time will be longer for the “all genes” matrix. Therefore it is advisable to select the “metabolic genes” option when searching metabolic genes.