The interrogation of specific transcripts using the redefined probe sets. The top panel shows the annotation of Affymetrix probes to AceVew transcripts, drawn by BLAT . The Affymetrix probe set "33631_at" (on GeneChip U95Av2) contains 16 probes; 9 probes match two transcript variants (d and e) of TXNL4A, forming a new probe set by our definition (circled in blue); and the remaining 7 probes match the variants a, d, f and I, forming another new probe set (circled in red). The bottom panel of the figure shows the log-based 2 signals for each probe in the treatment and control groups (3 samples in each group). The probes on x-axis were ordered from 5' to 3' of the gene. Notice that the expression values are relatively homogeneous within each new probe set (separated by the vertical line, and the target transcripts were also circled in blue or red). The expression level differences between two groups are most clearly seen in the group on the left side (circled in blue).