An analysis of intra array repeats: the good, the bad and the non informative

Here we present an analysis of all the cases of multiple probe sets measuring the same gene on the Affymetrix U133a GeneChip and found that although in the majority of cases both measurements tend to agree there are a significant number of cases in which the two measurements differ from each other. In these cases the measurements can not be simply averaged but rather should be handled individually.Our analysis allows us to provide a comprehensive list of the correlation between all pairs of probe sets that are mapped to the same gene and thus allows microarray users to sort out the cases that deserve further analysis. Comparison between the set of highly correlated pairs and the set of pairs that tend to differ from each other reveals potential factors that may affect it.High density DNA microarrays are extensively used by biologists in order to gain information about the expression levels of thousands of genes simultaneously. The advantage of the genomic approach is that it allows the study of cell behavior on the systems level rather than on the gene specific level [1]. One of the hurdles of this approach is that the confidence one has in each measurement is lower in comparison to the confidence gained by classical molecular biology techniques[2], thus extensive statistical analysis is needed in order to define the significance of the results. One of the approaches used to asses the quality of results is comparison between replicates [3]. This is accomplished by both printing each DNA fragment several times on the array (internal replicates) and repeating the experiment multiple times (experimental replicates). While internal replicates usually give very similar results, experimental replicates may differ from one another due to variation in the biological samples, exact experimental conditions and array processing [4]. There is yet another type of replicates – multiple array spots that are mapped to different regions of the same gene, thus allowing multiple measu