Evaluation of gene expression in Wilms' tumor tissue. The comparison of SAGE and Affymetrix duplicate samples demonstrates the reproducibility in both platforms (A, B). In addition, gene expression was compared between platforms (C) and showed a wide range of variation. The frequency distributions of gene expression values the final data sets do not differ from the total distributions (D). A: Comparison of a SAGE versus a LongSAGE library of the same sample Blue dots represent tag counts that are significantly different between the two libraries (according to the Z-test, Kal et al. 1999), green and red dots represent tag counts that do not differ between libraries. The red spots are tag counts that do not significantly differ from tag count 0 within the specified library (See also Table 4). B: Comparison of a duplicate analysis of one Wilms tumor sample using Affymetrix HG-U133A GeneChips. Gray spots represent probe sets that have an absent call. C: Comparison between SAGE and Affymetrix GeneChips for the Wilms' tumor sample. Red spots represent the total matching data set (n = 6408) and black spot represent the final selection (n = 1094). D: Frequency distribution of the Affymetrix intensity and SAGE tag counts from the final matched data set (1094 Unigene clusters) and the total matching data set. The smoothed line represents the distributions of the total data set in each platform. For both Affymetrix (classes with an intensity width of 10) and SAGE (classes based on tag counts) the distributions of the final data set and the total data set do not differ from each other (Chi-square values of 327 (df = 323; P = 0.412) and 104 (df = 105; P = 0.506), respectively).
van Ruissen et al. BMC Genomics 2005 6:91 doi:10.1186/1471-2164-6-91