Additional file 3.

Scatter plot of IHC staining intensity and gene expression levels determined by Affymetrix and Agilent array for LCM cells. Statistical Pearson correlation ranged from 0.26 – 0.57 and Spearman Coefficients ranged from 0.25 – 0.43. There was no positive correlation of immunolocalization data with array data for LCM stromal cells assayed by either Agilent or Affymetrix. Pearson correlation for LCM luminal cells was 0.57 and Spearman coefficient was 0.43, which were the same values as that for MACS-sorted luminal cells using updated probe set definitions. Pearson correlation between LCM stromal cell data and MACS-sorted stromal cell data assayed by Affymetrix array was 0.68, Spearman coefficient was 0.78. Pearson correlation between LCM stromal cell data analyzed by Agilent array and Affymetrix MACS-sorted stromal cell data was 0.65, Spearman coefficient was 0.55. Pearson correlation between LCM stromal cell data analyzed by Agilent array and Affymetrix LCM stromal cell data was 0.33, Spearman coefficient was 0.59.

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Pascal et al. BMC Genomics 2008 9:246   doi:10.1186/1471-2164-9-246