Start Validating microarray data using rt real time pcr

Validating microarray data using rt real time pcr

Genes are ranked from lowest to highest average log By careful analysis of the relevant databases (see Methods) we identified a subset of 31 genes for which the microarray probe-sets were deemed to recognize the exact same transcript or subset of transcripts as the q RT-PCR probes (Table ).

Genes are ranked from lowest to highest average log A comparison of average q RT-PCR, RMA, and MAS 5.0 scores and the corresponding correlation values for the 17 genes assayed in this study for which the Affymetrix microarray probesets (Affy IDs) may not recognize the exact same transcript subsets recognized by q RT-PCR probes.

Correlations with q RT-PCR data were obtained using microarray data that were processed using robust multi-array analysis (RMA) and the MAS 5.0 algorithm.

Our results indicate that when identical transcripts are targeted by the two methods, correlations between q RT-PCR and microarray data are generally strong (r = 0.89).

However, we observed poor correlations between q RT-PCR and RMA or MAS 5.0 normalized microarray data for 13% or 16% of genes, respectively.