RoPE: A robust profile likelihood method for differential gene expression analysis.

Variation in RNA-Seq data creates modeling challenges for differential gene expression (DE) analysis. Statistical approaches address conventional small sample sizes and implement empirical Bayes or non-parametric tests, but frequently produce different conclusions. Increasing sample sizes enable proposal of alternative DE paradigms. Here we develop RoPE, which uses a data-driven adjustment for variation and a robust profile likelihood ratio DE test. Simulation studies show RoPE can have improved performance over existing tools as sample size increases and has the most reliable control of error rates. Application of RoPE demonstrates that an active Pseudomonas aeruginosa infection downregulates the SLC9A3 Cystic Fibrosis modifier gene.

Correction to: Correlation of 3T multiparametric prostate MRI using prostate imaging reporting and data system (PIRADS) version 2 with biopsy as reference standard.

Unfortunately the article was published with a spell error in the co-author name "Hassan Maan". The correct co-author name should be "Hassaan Maan".

Correlation of 3T multiparametric prostate MRI using prostate imaging reporting and data system (PIRADS) version 2 with biopsy as reference standard.

OBJECTIVE: To correlate the findings on 3T multiparametric prostate MRI using PIRADS version 2 with prostate biopsy results as the standard of reference. MATERIALS AND METHODS: 134 consecutive treatment naive patients (mean age 64 years, range 41-82 years) underwent MRI-directed prostate biopsy. MRI-TRUS fusion biopsy was used for 77 (77/134 = 57.5%) patients, cognitive fusion for 51 (51/134 = 38.0%) patients, and 6 patients (6/134 = 4.5%) without a target nodule had systematic biopsy only. Out of the 1676 biopsy sites, 237 (237/1676 = 14.1%) were positive on MRI for a PIRADS 3, 4, or 5 nodule. Fifty-eight (58/134, 43.3%) patients had clinically significant prostate cancer (csPCa). The findings on MRI using PIRADS version 2 were correlated with the biopsy results. RESULTS: The accuracy, sensitivity, specificity, positive predictive value, and negative predictive value of PIRADS ≥ 3 for csPCa were 89%, 76.5%, 89.7%, 31.7%, and 98.4%, respectively. The detection rates of csPCa for PIRADS 3, 4, and 5 nodules were 6.1% (4/66), 33.3% (42/126), and 64.4% (29/45), respectively. MRI did not identify a nodule in 23/1676 (1.4%) biopsy sites that contained csPCa. The MRI reader, biopsy operator, method of fusion biopsy, and zonal location of prostate nodule did not significantly affect the odds of having a biopsy result positive for csPCa. CONCLUSION: PIRADS ≥ 3 had high specificity and high negative predictive value for csPCa using biopsy results as the standard of reference. The presence of csPCa from a biopsy site was highly unlikely in the absence of a corresponding PIRADS ≥ 3 nodule.