Figure 1

An example of grouping Affymetrix probes into new probe sets. The top panel shows an AceView diagram demonstrating an example of the regrouping strategy. The Affymetrix probe set "34666_at" (on GeneChip U95Av2) contains 16 probes; 5 probes forming the newly defined probe set b0805_9681 match all three transcript variants (b, c, and i) of SOD2; and 8 probes (b0805_616) match the variants b and c; and the remaining 3 probes (b0805_11137) were mapped to the variant b only. The blue vertical line indicates the exon-intron boundaries or the beginning and ends of transcripts. The bottom panel of the figure shows the log-based 2 signals in the treatment and control groups for each probe. The values from all six samples were drawn here. The probes on x-axis were ordered from 5' to 3' of the gene.