Affymetrix Gene Expression Analysis

Affymetrix expression data for LAMP2 and S100A6 genes in patient samples were produced from publicly available data sets. The CEL files for the tumour samples were downloaded from the Gene Expression Omnibus (GEO) database (http://www.ncbi.nlm.nih.gov/geo/), data series GSE2109. Normal tissue data were from the GEO data series GSE7307, Human Body Index. The CEL files were processed and analysed using the MAS 5.0 algorithm (Affymetrix) and screened through a rigorous quality control panel to remove samples with a low percentage of probe sets called present by the MAS 5 algorithm, indicating problems with the amplification process or poor sample quality; high scaling factors, indicating poor transcript abundance during hybridization; and poor 30/50 ratios, indicating RNA degradation either before or during processing. The remaining samples were normalized to the trimmed average of 500 in the MAS 5 algorithm before comparison of the expression values across tumours and normal samples46 (link).