On the necessity of different statistical treatment for Illumina BeadChip and Affymetrix GeneChip data and its significance for biological interpretation

Table 4 Cell cycle genes in the MT1-MMP data.

		σ _μ [7]		σ _wtrep
Gene Symbol	RefSeq ID	log₂FC	p value	log₂FC	p value	Gene Description
CCNA1	NM_003914	-	≥ 0.05	1.12	0.00	Cyclin A1
CDC45L	NM_003504	-	≥ 0.05	1.05	0.00	CDC45 cell division cycle 45-like
CCNB1	NM_031966	1.30	< 0.05	1.44	0.00	Cyclin B1
CCNB2	NM_004701	1.27	< 0.05	1.39	0.00	Cyclin B2
CDC2	NM_033379	1.10	< 0.05	1.20	0.00	cell division cycle 2, G1 to S and G2 to M
CDC20	NM_001255	2.02	< 0.05	2.01	0.00	Cell division cycle 20 homolog

The first, second and last column indicate the gene symbol, the RefSeq ID and the description of each cell cycle gene respectively. The third and fourth columns indicate the logarithm fold change and the P-value of each gene found by Golubkov V.S. et. al. [7], which is analogous to using σ_μas the summary statistic. The fifth and sixth columns indicate the logarithm fold change and the P-value of each gene found by using σ_wtrepas the summary statistic. Cutoff criteria of p ≤ 0.05 and |FC| ≥ 2 were applied. The genes in the upper section were found only by the σ_wtrepstatistic, whereas the genes in the lower section were detected with significance by both statistics.

ISSN: 1745-6150