PMC

Distribution of the number of overlapping probes between probe sets on the Hu133A Affymetrix chip and the clones serving as probes on the Agilent Human 1 cDNA microarray. The number of overlapping probes for each probe set was calculated as described in the text.

Overlapping probes show increased correlation between gene expression measurements produced by the Affymetrix Hu133A chip and the Agilent Human 1 cDNA microarray. Relative expression ratios were measured and calculated while comparing RNA from the cell cultures MDA-MB-436 and HMEC and from the cell cultures HCC1954 and HMEC. Aliquots of the same RNA sample were hybridized to different platforms. Relative expression was calculated at the level of individual probes on the Affymetrix platforms. Pearson correlation coefficients were calculated between ratios determined by individual Affymetrix probe intensities and the ratios obtained from cDNA microarray. Correlation coefficients were determined for different subsets of probes including overlapping PM, overlapping MM, non-overlapping PM and non-overlapping MM.

Sequence-matched probe sets provide more consistent classification results derived from breast cancer associated gene expression data sets obtained by different types of microarray platforms. Hierarchical clustering of two different subsets of genes taken from the data set published by West et al. (). (Top) The result using the 293 genes as suggested by Sorlie et al. () after matching genes between the Affymetrix and cDNA microarray platforms using Unigene IDs. (Bottom) The clustering result by reducing the gene set to only those that are also sequence-matched between the two platforms. The color code of the samples was assigned as described in Sorlie et al. (,).