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Microarray technology has been widely applied in the research
area of animal genetics and breeding. In the earlier stage of microarray data
analysis, the non-specific filtering is a common procedure which has been used
increase the detection rate of differentially expressed genes. In this investigation,
researchers use the data from Affymetrix GeneChip Porcine Genome Array to comparatively
assess the effects of different non-specific filtering methods on the results
of transcriptome analysis. The research results showed that the MAS5, ET and
IQR filters could increase but the I/NI-calls method could decrease the number
of differentially expressed genes. Here into, the IQR filter has the largest
detection rate. Furthermore, the two-way combinations with IQR filter have the
similar increasing effect on differentially expressed gene detection. It is
concluded that not all non-specific filtering methods could increase the detection
rate in microarray data analyses and the IQR filter could be considered as a
preferred choice when improvement in the detection rate is needed on some occasions.
