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Figure 4 | Genome Biology

Figure 4

From: An investigation of biomarkers derived from legacy microarray data for their utility in the RNA-seq era

Figure 4

The percentages of probe sets in mapping groups A, B, C, and D. The percentages of Affymetrix probe sets in four mapping groups A, B, C, and D for the six RNA-Seq gene sets are shown in stacked bar charts. The data set comprises 62 Affymetrix Rat_230_2 arrays and 62 RNA-Seq assays from the same set of 62 rat liver RNA samples. The microarray data were normalized with MAS5, and the same RNA-Seq raw data were analyzed by six independent data analysis teams with a variety of analysis pipelines, that is, P1 (NCBI Magic), P2 (Novoalign with RefSeq gene models), P3 (Bwa + RefSeq RNAs), P4 (Tophat + HTSeq with RefSeq gene models), P5 (Bowtie + RSEM with Ensembl gene models), and P6 (Tophat + cufflinks de novo assembly). The Affymetrix probe sets (31,099 in total) were separately mapped to the six RNA-Seq gene sets. The mappings to P1, P2, P3, and P4 gene sets are based on the gene ID mapping approach, while mappings to P5 and P6 gene sets are based on the genome location mapping.

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