BioMed Research International / 2009 / Article / Fig 4

Methodology Report

Automation of cDNA Synthesis and Labelling Improves Reproducibility

Figure 4

Dendrogram and heat maps of interplatform correlations. (a) is based on the 12091 probes common to all platforms (based on the mapping procedure in the MAQC study). A distinct clustering of platforms based on identical probes manufactured by Operon is apparent (KTH_Auto, KTH_Man, NCI.1–3). The one-colour platforms (GEH, ABI, AG1, ILM, AFX) were generally more highly correlated than two-colour platforms (NMC, NCI, BIO, KTH). (b) is based on a subset 906 probes for which TaqMan-based relative expression levels are available. Generally, the one-colour platforms are clustered closer to the TaqMan experiment. Interestingly, the NCI.4 experiment is positioned somewhat ambiguously in the two dendrograms, possibly indicating some uncertainty in the dendrograms.

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