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.
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

Dallas et al. BMC Genomics 2005 6:59   doi:10.1186/1471-2164-6-59