Harold Pimentel and Lior Pachter submitted to the webtool the results of running the eXpress algorithm on the ENCODE GM12878 dataset which performed better than what is reported in the paper. While looking into the reason for this discrepancy we found two errors in our paper. First, the commands and parameter settings provided in the log information on the webtool were incorrect. Second, we realized that we ran the eXpress submission differently than the other methods for this particular dataset. One cause for the discrepancy was the accidental use of a different transcript FASTA file. We reran eXpress controlling for these differences and confirmed that better results are attained (click "ENCODE: 2 reps, high depth" tab on webtool). The comparative figure for GM12878 are below:
The following four sentences in the paper should have read:
Performance was generally poor, with one methods clearly underperforming and RSEM slightly outperforming the rest.
In the first dataset, Flux Capacitor clearly underperforms compared with the other methods in the regions with most data (A between 3 and 8).
Here we see Flux Capacitor underperforming and RSEM slightly outperforming the other methods in the simulation dataset.
With the exception of the underperforming Flux Capacitor, we found that the other algorithms performed similarly.
We apologize for this error and have contacted the journal.