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Table 2 Correlation of quantification method predictions with MAQC qRT-PCR values

From: RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

SRA ID Read type Sample RSEM IsoEM IsoEM (C) Cufflinks Cufflinks (C) rQuant
SRX016366 SE HBR 0.69 0.68 0.68 0.71 0.79 0.72
SRX003926 SE HBR 0.68 0.67 0.67 0.7 0.73 0.71
SRX018974 PE HBR 0.69 0.69 0.69 0.69 0.78 NA
SRX016368 SE UHR 0.71 0.71 0.72 0.72 0.77 0.72
SRX016369 SE UHR 0.73 0.74 0.74 0.73 0.76 0.74
SRX016370 SE UHR 0.74 0.75 0.75 0.74 0.77 0.75
SRX016371 SE UHR 0.74 0.75 0.75 0.74 0.77 0.75
SRX016372 SE UHR 0.75 0.75 0.75 0.74 0.77 0.76
SRX003927 SE UHR 0.72 0.71 0.72 0.71 0.74 0.72
  1. Correlation values (Pearson r2 of log-transformed abundance values) were computed between the predictions of four methods and "gold-standard" values from qRT-PCR for nine different RNA-Seq data sets. IsoEM and Cufflinks were run with (C) and without their bias correction modes.