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Table 3 Pearson's correlations between Affymetrix and Codelink data

From: Transcript-based redefinition of grouped oligonucleotide probe sets using AceView: High-resolution annotation for microarrays

Cross-platform Comparison   Pearson's correlations
  N D1/C1 D2/C2 D3/C3
UniGene-based match 7,399 0.55 0.55 0.58
AceView-based match 4,064 0.55 0.57 0.61
   Probe sets with size ≥ 4 3,694 0.59 0.61 0.63
   Probe sets with size < 4 370 0.34 0.37 0.39
RefSeq-based match* 7,801 0.60 0.61 0.64
  1. The D1-D3 and C1-C3 are replicates in the treatment group and the control group respectively. The correlation is calculated on log-ratios, where the pairing of technical replicates is arbitrary. The best concordance between two platforms was observed using AceView-based transcript-level probe sets (with size ≥ 4) and RefSeq based probe sets.
  2. *Using RefSeq-based mappings by Dai et al [13]