Simultaneous genome-wide gene expression and transcript isoform profiling in the human malaria parasite
Fig 2
Differentially expressed genes are replicated with high concordance on the exon arrays.
Log2 ratios of 12 hpi vs. 36 hpi samples were calculated to determine differentially expressed genes. The correlations between log2 ratios on the Nimblegen and Agilent HD exon (0.905, A and C) and Agilent 15K arrays (0.873, B and D) show that biologically relevant information is replicated across array platforms. The mean differential expression values are comparable between chip platforms, though both Agilent arrays have an overall larger dynamic range (C and D). The correlation between the Agilent 15K and Agilent HD exon array is 0.676 (E). Different biological samples were hybridized to these two arrays and the correlation value matches that of these two biological replicates when hybridized on the same platform (F, 0.692) suggesting that the variation seen is due to differences in the samples.