Additional file 2: Figure S2. of Multi-platform assessment of transcriptional profiling technologies utilizing a precise probe mapping methodology

Overall average absolute fold-change comparisons across platforms with entire set and transcript pattern (TP) defined subset data, with a focus on the effect of Affymetrix “Signal Space Transformation” (SST) algorithm on the overall platform fold-change magnitude. The SST, in conjunction with the regular robust multiple-array average normalization method (SST-RMA, the dark blue bars), was able to improve the fold-change in the HTA2.0 arrays, and provided a 2-5x greater fold-change estimates overall, as compared to conventional data processing method (regular RMA, the light blue bars). (TIFF 491 kb

Additional file 1: Figure S1. of Multi-platform assessment of transcriptional profiling technologies utilizing a precise probe mapping methodology

Box-Whisker plot for illustration of fold-change variability in each platform. (A) and (B) are for fold-change data in the 4 sample titrations in entire set and transcript pattern (TP) defined 7,034 RefSeq genes subset data, respectively; (C) and (D) are for fold-change data at overall platform level in the entire set and TP-defiend subset data, respectively. The frame boxes are the inter-quartile range (i.e. 25 % to 75 %). (TIFF 867 kb