Figure 7

Isoform switching increases the False Positive Rate (FPR) of differential expression. If at a gene locus the expressed isoform changes, this leads to an increase in the false positive detection of differential expression based on gene-level counts. For set of significance thresholds we plot the FPRs in the absence and presence of isoform switching. False Positive Detection can only be avoided if expression counts are normalized for isoform length as is the Transcripts-per-Million (TPM) score returned by RSEM.