Table 2.

The R² correlation coefficient of estimated expression levels and ground truth

Expression	Cutoff	BitSeq	Cuff. 0.9.3	RSEM	MMSEQ
Transcript	1	0.994	0.764	0.995	0.997
Relative	10	0.945	0.724	0.876	0.886
Relative	100	0.963	0.773	0.946	0.948
Gene	1	0.994	0.823	0.996	0.998

Three different expression measures were used: absolute transcript expression, relative within-gene transcript expression and gene expression. Comparison includes sites with at least 1 read per transcript for transcript expression, either 10 or 100 reads pre gene for within-gene transcript expression and at least 1 read per gene for gene expression. The highest correlation is in bold.