Figure 3

Performance of the GS FLX transcriptome sequencing evaluated using the MAQC metrics for reproducibility and accuracy. (a) The reproducibility of the ExpressSeq gene counts is displayed using a scatterplot of the numbers of unique hits for different RefSeq genes counted in two sequencing regions on the same sequencing plate using the TSEQ sample preparation method. The total numbers BLAST hits to RefSeq genes in each region were 153,697 and 139,962. The solid blue line indicates the ideal result of equal fractions of gene hits for each sequencing region and the two solid, yellow and red, curves show the median CV's ~ predicted by the Poisson sampling error model. (b) The relative accuracy of the ExpressSeq gene counts is illustrated with a scatterplot of the log base 2 fold-changes (FC) in gene expression levels for the MAQC A and B samples on the y-axis compared with the TaqMan measurements from the original MAQC study on the x-axis for 217 RefSeq genes that were called "present" in both samples by TaqMan and the microarray platforms. The trendline shows the best fit with Pearson correlation R² = 0.81.