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Fig. 4 | Genome Biology

Fig. 4

From: Isoform prefiltering improves performance of count-based methods for analysis of differential transcript usage

Fig. 4

Performance stratified by isoform dominance. The degree of isoform dominance (the difference in relative abundance between the two most highly expressed isoforms of a gene, indicated in the panel headers as e.g. [0.000,0.333)) is the main determinant of the methods’ ability to detect differential isoform usage in our simulations (recall that the differential isoform usage was introduced by switching the abundances of the two most dominant transcripts of 1000 selected genes). DTU for genes where the two differentially used isoforms are expressed at almost the same level (left panels) is more difficult to detect than genes with one dominant isoform (right panels). On the other hand, the FDR control in the latter category is very poor for most methods. The total number of genes (n) and the number of genes affected by DTU (n.ds) in each category are indicated in the panel headers

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