Comparison of uniqueness compensation methods for RNA-Seq.

<p>Scatter plots showing how gene expression values (RPKM) are affected by uniqueness compensation for transcripts as a function of increasing proportion unique positions. (<b>A</b>) Uniqueness compensation with MULTo corrected transcript lengths are close to optimal compensation line (y = 1/x) (<b>B</b>) ERANGE uniqueness compensation. (<b>C</b>) Cufflinks uniqueness compensation. (<b>D,E</b>) MA-plots between MUL and ERANGE uniqueness compensation (D) and between MUL and cufflinks uniqueness compensation (E) showing how gene expression differences correlate to the gene expression average. Short transcripts were colored red.