Pseudo-precision in gene expression values can reduce efficiency.
OBJECTIVE
When estimating the expression of genes based on the scanned images from microarrays various algorithms are applied in a so-called low-level analysis which can calculate expression values with an arbitrary number of digits beyond the decimal point. However, too many digits (decimal places) are usually not justified because they do not represent the precision of the measured expression. Thus, there is pseudo-precision and, as a result, there are no tied values.


METHODS
We suggest avoiding, or omitting, the pseudo-precision: ties can remain, or be created by rounding the computed expression values. Then, average ranks can be used in order to apply nonparametric tests when ties occur. We use two actual data sets and the Wilcoxon rank sum test.


RESULTS
We demonstrate that rounding gives a more efficient test, i.e. the average p-value is decreased and the number of p-values smaller than 0.05 is increased.


CONCLUSIONS
The random noise of pseudo-precision can reduce the efficiency of statistical tests applied to detect differentially expressed genes. This result is, obviously, relevant in many other areas of our digitalized world.
Neuhäuser
M
M
Institute for Medical Informatics, Biometry and Epidemiology, University Hospital Essen, Germany. neuhaeuser@rheinahrcampus.de
Boes
T
T
Jöckel
K-H
KH
D003627:Data Interpretation, Statistical; D015870:Gene Expression / Q000235:genetics*; D006801:Humans; D015233:Models, Statistical; D020411:Oligonucleotide Array Sequence Analysis; D018709:Statistics, Nonparametric