Table 1

Comparison of the methods for probe set matching. In the case of Best Match, the relation of probe sets between U95Av2 and U133A is many-to-one. The Pearson correlation coefficients of array pairs from the same biopsies were calculated and averaged for the assessment of comparability. The main reason for the high comparability of Best Match is the selection of the most appropriate probe set from the multiple matches using sequence information.

No. of matched probe sets (U95Av2)

No. of matched probe sets (U133A)

No. of unique IDs shared between U95Av2 and U133A

Mean correlation coefficient of array pairs

UniGene IDs

11,596

15,858

8,867

0.832 ± 0.017

LocusLink IDs

11,389

15,666

8,661

0.831 ± 0.017

Best Match

10,507

9,530

9,530

0.870 ± 0.016

Hwang et al. BMC Bioinformatics 2004 5:159   doi:10.1186/1471-2105-5-159