Cross-platform comparison of Affymetrix and spotted cDNA expression profiles using CIA. The first two axes of a CIA of gene expression profiles of the complete gene set from the Ross spotted cDNA array dataset (closed circles) and 1517 genes from the Staunton Affymetrix dataset (arrows) are shown. Circles and arrow represent the projected co-ordinates of each dataset, and these are joined by a line, where the length of the line is proportional to the divergence between the different gene expression profiles. The cell lines are coloured as in Figure 1. The cell lines are derived from breast (BR), melanoma (ME), colon (CO), ovarian (OV), renal (RE), lung (LC), central nervous system (CNS, glioblastoma), prostate (PR) cancers and leukaemia (LE). Colon and leukaemia cells were separated from those with mesenchymal or stromal features (glioblastoma and renal tumour cell lines) on the first axis (F1, horizontal), and melanoma cell lines were distinguished from the other cell lines on the second axis (F2, vertical). A histogram of the main factors which explain the total variability of this CIA is superimposed on the top right corner. The first three axes represented 42%, 21% and 8% of the inertia.