1. Consistency Assessment among Redundant Probe Sets Interrogating the Same Gene on the Affymetrix MOE430 GeneChip Department of Biostatistics, Section on Statistical Genetics University of Alabama at Birmingham Birmingham, AL 35243 Xiangqin Cui

2. BMC Bioinformatics 2007, 8:13

3. Genome based probe set grouping (GG) Affy Annotation Match refseq ids Affy grouping (AG) Redundant probe sets # of redundant prs/gene # of Genes (AG) # of Genes (GG) 111,11023,459 25,1333,767 32,4271,173 41,181353 5556138 63050 71440 8690 9300 10150 1170 1240 1330 1510 Total20,98428,890 Probe set grouping (Mouse 430 GeneChip)

4. Total # of genesP/PA/AA/P GG (3767)18848231060 (28%) AG (5133)166417941675 (33%) 1) P/A call consistency Not Sig.Sig. Not sig.192781 Sig.104163 Probe set 1 Probe set 2 Significance level is FDR 0.005. Data are from the genes with 2 probe sets per gene according to the GG grouping. 2) Significance consistency of present redundant probe sets StatisticsAGP(AG)GGP(GG) Corr. Coef.0.650.790.750.82 % genes w/ opposite directions 0.330.230.270.21 3) Fold change consistency Example data: PKD data (7 severe vs 7 mild pkd mice using kidney)

5. R=0.91; about 0.02% of genes with different FC directions (Cryl1 crystallin lambda 1 [ Mus musculus ] )

6. Future Work Establish a gene model based analysis in contrast to the current probe-set based analysis To achieve that, we need to 1)Annotate all the probe sets and probes in relation to the gene structure 2)Relationship among redundant probe sets 3)The causes for the different behavior of redundant probe sets 4)Annotate more chips and more platforms 5)Establish software Acknowledgements: Dr. Ann Lorain SSG/Biostatistics and Genetics Dr. Michal Mrug, Medicine/GTM Dr. Lisa Guay-Woodford, Genetics