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Table 2 A comparison of average qRT-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 qRT-PCR probes. Genes are ranked from lowest to highest average log2 RMA scores. Genes with significant correlations (p < 0.05) obtained by either normalization procedure are highlighted in bold. The number of specimens tested for each gene is included (n). Expression levels are shown as log2.

From: Gene expression levels assessed by oligonucleotide microarray analysis and quantitative real-time RT-PCR – how well do they correlate?

GENE   EXPRESSION CORRELATION
NAME AFFY ID n RMA MAS 5.0 qRT-PCR RMA-qRT-PCR MAS-qRT-PCR
CDC14A 210742_at 13 5.77 7.64 -0.67 0.31 0.26
P125 209175_at 19 6.61 8.43 0.54 0.11 -0.11
GCLC 202922_at 13 6.65 9.20 0.33 0.46 0.56
MAP3K7 206853_s_at 13 6.65 8.72 1.19 0.11 -0.10
TIAL1 202405_at 19 6.68 7.86 0.30 0.32 0.17
FLJ20003 219067_s_at 19 6.71 8.54 0.64 0.64 0.34
RUNX1 210365_at 13 6.95 9.24 1.47 0.29 0.28
PLEKHA1 219024_at 19 6.99 8.18 -2.88 -0.40 -0.28
FLJ12661 218420_s_at 19 7.35 8.50 0.57 -0.08 -0.17
RGC32 218723_s_at 19 7.36 8.11 -3.20 0.85 0.96
WDR11 218090_s_at 19 7.96 9.04 0.60 0.12 0.01
RFC3 204127_at 19 8.10 9.77 1.20 0.62 0.64
ASAH1 213702_x_at 22 8.30 10.29 1.46 0.29 0.27
P38IP 220408_x_at 19 8.35 9.55 0.76 0.73 0.65
BUB3 201456_s_at 19 8.41 9.70 0.60 0.64 0.61
SAC2 203607_at 19 8.86 10.21 0.35 0.22 0.12
TSC22 215111_s_at 19 10.56 11.87 -1.34 0.83 0.82