Effects of Multiple Probesets in Affymetrix GeneChips on Identifying Differentially Expressed Genes in iPS Cells

There are multiple probesets that correspond to a gene in Affymetrix GeneChip plat- form. Different combination and annotation methods will lead to different results of expression when we transform the information from probesets to genes. In this work, we collected seven methods to interpret the multiple probesets for representing a gene. We compared these methods and identified their effects on the identification of differential genes. Specifically, we focused on the analysis of differential genes between iPS cells and ES cells. We identified their differences by calculating the t-test p-values and Pearson correlation coefficients. Our results show that gene expression by different methods of combining the multiple probesets results in slight differences of differential genes in iPS cells. We also identified the effects on coexpression in key transcrip- tion factors of iPS cells. The results indicate that adopting different methods to handle multiple probesets is important for accurate estimation of gene expressions.