Performance comparison of two microarray platforms to assess differential gene expression in human monocyte and macrophage cells

Table 1 Results of the differential expression analysis

Microarray Platform	Pc < 0.001^#	Pc < 0.05 & FC > 2^##	Best 3800 probes^###
Affymetrix	1877 genes (1908 probe sets)	1914 genes (1945 probe sets)	3738 genes 0.05 < Pc < 10^-11 0.48 < \|log 2 FC\| < 10.38
Illumina	1993 genes (2010 probes)	845 genes (854 probes)	3761 genes 0.05 < Pc < 10^-11 0.26 < \|log 2 FC\| < 6.92
Reference list (RNG-86)	5204 genes (5677 probes)	894 genes (933 probes)	3552 gene 0.05 < Pc < 10^-79 0.34 < \|log 2 FC\| < 6.91

Number of differentially expressed genes between macrophage and monocyte samples using different criteria for selecting lists. The analysis was performed on the subset of well-matched transcripts common to the three platforms [see Additional file 5] for the number of probes included in this analysis for each platform).
# adjusted P-value (Pc) of the moderated t test.
## adjusted P-value of the moderated t test combined to fold change (FC).
### best overlapping lists of genes among platforms (see results section for details).

ISSN: 1471-2164