Fig. 3

Gene expression analysis of five cancer cell in the presence of WBC background. A Responses to increasing amounts of total RNA from five different cell lines for probes to four different genes in the presence of 1 ng of WBC total RNA. For each probe the medians of nine no template control samples were subtracted from the cell line data to obtain net signals, and the results are plotted as in Fig. 2A. B Principal Components Analysis of the data from 15 genes assayed with five different amounts of total RNA from five different cell lines in a background of 1 ng of WBC RNA. The data were mean centered and scaled for clustering. C Hierarchical clustering of the data from 15 genes assayed with 20 pg of total RNA from five different cell lines in a background of 1 ng of WBC RNA. Data were log2 transformed, and then the data for each probe in the columns were mean centered; the data were not scaled, so some genes may have had more influence on clustering than others. The distance method used for hierarchical clustering was non-parametric rank order Kendall correlation and the linkage method used was Ward.D2