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Table 1 Results of the differential expression analysis

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

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

  1. 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).
  2. # adjusted P-value (Pc) of the moderated t test.
  3. ## adjusted P-value of the moderated t test combined to fold change (FC).
  4. ### best overlapping lists of genes among platforms (see results section for details).
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BMC Genomics

ISSN: 1471-2164

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