Table 2.

Correlation of gene level analysis between the human GWSA and the Affymetrix HG-U133 Plus2.0 array.

Genes included	# of Genes represented	Correlation
all Genes	7,147	0.85
1.5 Fold Change (FC)	3,382	0.90
2.0 FC	2,036	0.92
3.0 FC	1,036	0.933

As intensity values were significantly different due to different formats, we compared the fold change between the universal reference (sample A) and brain (sample B) between the two designs. The correlation between the two platforms was higher when genes that were found to be differentially expressed were considered distinctly, as would be expected where genes showing no differential expression would exhibit a higher variability.