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. 2013 Sep 13;14(Suppl 11):S8. doi: 10.1186/1471-2105-14-S11-S8

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Copyright © 2013 Wu et al; licensee BioMed Central Ltd.

This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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Statistics for comparing RNA-seq-based fold-changes and RT-qPCR-based fold-changes vary with different annotations. The comparison of fold-change estimates between RNA-seq and RT-qPCR using two RNA-seq expression estimates and three statistics. (a) TPM estimates are produced by the OSA package. (b) FPKM estimates are generated by Cufflinks with TopHat alignment. The RefSeq annotation always has the lowest (1) average absolute deviation and (2) root mean square error, and the highest correlation coefficient when treating RT-qPCR estimates as the ground truth.