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Table 2 Comparison of the power and type I errors for a simulated microarray dataset

From: BABAR: an R package to simplify the normalisation of common reference design microarray-based transcriptomic datasets

 

Normalisation method

 

Scale

BABAR

Quantile

print-tip loess

No. of genes

Power

Error

Power

Error

Power

Error

Power

Error

118

0.66

0.022

0.62

0.030

0.51

0.032

0.48

0.033

220

0.73

0.034

0.58

0.053

0.57

0.051

0.51

0.056

407

0.77

0.055

0.62

0.088

0.61

0.089

0.56

0.091

756

0.82

0.088

0.67

0.150

0.65

0.158

0.63

0.163

1402

0.87

0.144

0.76

0.260

0.74

0.300

0.71

0.314

  1. The power and proportion of type I errors for a dataset consisting of 6 simulated microarrays [23] were calculated via the samr R package [25]. Analysis followed one of four methods of microarray data normalisation for different numbers of differentially expressed genes. For BABAR, analyses were run after background correction (subtraction) with 'within arrays' block-by-block centering of the medians, 'between arrays' cyclic loess with averaging of the log2-ratios, and final median centering of the data. For the other methods, analyses were run after the data were background corrected (normexp) with a 'within arrays' method for data centering (printtiploess), followed by the appropriate 'between arrays' method (none, quantile or scale normalisation).