Table 3:

Percentage of low-correlation probes for different methods

Annotation Methods	Correlation  < 0.20 (%)	Correlation  < 0.40 (%)
Vendor	3.8	14.3
Bioconductor	3.3	13.8
BLAST	3.1	13.0
Consensus	2.5	11.3

All probes on both Affymetrix U133 Plus 2 and Illumina Human Genome v3 platforms were mapped to Entrez IDs using four different annotation methods, and then two platforms were aligned using Entrez IDs. Entrez IDs (4915) that appear in all four mapping methods and have expression values (in log2 scale) >7 on both platforms were included as the total count for all four methods in this table.