An analysis of intra array repeats: the good, the bad and the non informative.
BACKGROUND
On most common microarray platforms many genes are represented by multiple probes. Although this is quite common no one has systematically explored the concordance between probes mapped to the same gene.


RESULTS
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.


CONCLUSIONS
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.
Elbez
Yedid
Y
Faculté des Sciences de la vie., Université Louis Pasteur 28 rue Goethe., 67083 Strasbourg cedex, France. yedid.e@gmail.com
Farkash-Amar
Shlomit
S
Simon
Itamar
I
D003627:Data Interpretation, Statistical; D020869:Gene Expression Profiling / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D015203:Reproducibility of Results