Table 2

Rank correlations of liver Ct values identifies effects of oligo d(T) primers vs. random hexamer primers.

Unamplified

MessageAmp

NuGen

Version 1

Version 2

Version 1–2

2 Rounds V 1–2


MessageAmp

0.75

1

NuGen

0.65

0.83

1

Version 1

0.61

0.68

0.61

1

Version 2

0.84

0.92

0.78

0.71

1

Version 1–2

0.84

0.90

0.84

0.67

0.95

1

2 Rounds V1–2

0.79

0.89

0.81

0.67

0.93

0.92

1

Degraded V1–2

0.85

0.85

0.77

0.71

0.89

0.91

0.85


Rank cross-correlation matrix for liver Ct values. The mean cycle threshold (Ct) values obtained with liver RNA samples were rank-ordered and correlated. Results indicate the faithful reproduction of an ordered list of mRNA concentrations in liver RNA before and after amplification. Results were filtered for acceptable PCR efficiencies (see Methods), producing 138 primer pairs for this analysis. Methods using random primer (including unamplified RNA) are bold, those using oligo d(T) are italicized. Scatter plots of each rank Ct correlation are available at: http://cord.rutgers.edu/amplification/index.html webcite

Goff et al. BMC Genomics 2004 5:76   doi:10.1186/1471-2164-5-76

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