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Table 1 Correlation of underlying expression level and inferred abundances for different approaches

From: Transcript quantification with RNA-Seq data

Approach Correlation
  Across genes Within genes (mean)
Position-wise inference with transcript profiles 0.820 0.635
Segment-wise inference with transcript profiles 0.693 0.488
Position-wise inference without transcript profiles 0.684 0.540
Segment-wise inference without transcript profiles 0.580 0.367
  1. rQuant, which infers transcript abundances from read data at each position, is compared against a segment-based approach, which uses averages of averaged read counts at shared transcript segments. The correlation between true and inferred abundance was determined across all annotated transcripts; for alternatively annotated genes, the average of correlation within transcripts of each gene was calculated. We compare against not optimising the transcript profiles (i.e. uniform profiles).