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Fig. 2 | Genome Biology

Fig. 2

From: MPRAnalyze: statistical framework for massively parallel reporter assays

Fig. 2

Comparison of MPRAnalyze’s α estimate of transcription rate with the ratio-based estimates \(\left (\text {agg.ratio:} \frac {\frac {1}{n}\sum _{i}^{n} RNA_{i}}{\frac {1}{m}\sum _{j}^{m} DNA_{j}}; \text {mean.ratio:} \frac {1}{n}\sum _{i}^{n}\frac {DNA_{i}}{RNA_{i}}\right)\)a The variance measured among estimates of negative-control sequences in each dataset (these are assumed to have an identical transcription rate). b–d Barcodes were sampled and quantification was recomputed based on the partial data to measure the effect of barcode number on estimate performance [See “Methods” for further subsampling details]. Analyses were performed using the full-data estimate as the ground truth. e–g MPRA data was simulated to provide an actual ground truth. In each case we measured the bias (estimatetruth) (b,e); the standard deviation \(\left (\sqrt {Var\left (estimate-truth\right)}\right)\) (c,f); and the Spearman correlation between the estimates and the ground truth (d,g)

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