Advances in high-throughput sequencing on single-cell gene expressions [single-cell RNA sequencing (scRNA-seq)] have enabled transcriptome profiling on individual cells from complex samples. A common goal in scRNA-seq data analysis is to discover and characterise cell types, typically through clustering methods. The quality of the clustering therefore plays a critical role in biological discovery. While numerous clustering algorithms have been proposed for scRNA-seq data, fundamentally they all rely on a similarity metric for categorising individual cells. Although several studies have compared the performance of various clustering algorithms for scRNA-seq data, currently there is no benchmark of different similarity metrics and their influence on scRNA-seq data clustering. Here, we compared a panel of similarity metrics on clustering a collection of annotated scRNA-seq datasets. Within each dataset, a stratified subsampling procedure was applied and an array of evaluation measures was employed to assess the similarity metrics. This produced a highly reliable and reproducible consensus on their performance assessment. Overall, we found that correlation-based metrics (e.g. Pearson's correlation) outperformed distance-based metrics (e.g. Euclidean distance). To test if the use of correlation-based metrics can benefit the recently published clustering techniques for scRNA-seq data, we modified a state-of-the-art kernel-based clustering algorithm (SIMLR) using Pearson's correlation as a similarity measure and found significant performance improvement over Euclidean distance on scRNA-seq data clustering. These findings demonstrate the importance of similarity metrics in clustering scRNA-seq data and highlight Pearson's correlation as a favourable choice. Further comparison on different scRNA-seq library preparation protocols suggests that they may also affect clustering performance. Finally, the benchmarking framework is available at http://www.maths.usyd.edu.au/u/SMS/bioinformatics/software.html.

The increasing role played by liquid chromatography‐mass spectrometry (LC‐MS)‐based proteomics in biological discovery has led to a growing need for quality control (QC) on the LC‐MS systems. While numerous quality control tools have been developed to track the performance of LC‐MS systems based on a pre‐defined set of performance factors (e.g., mass error, retention time), the precise influence and contribution of the performance factors and their generalization property to different biological samples are not as well characterized. Here, a web‐based application (QCMAP) is developed for interactive diagnosis and prediction of the performance of LC‐MS systems across different biological sample types. Leveraging on a standardized HeLa cell sample run as QC within a multi‐user facility, predictive models are trained on a panel of commonly used performance factors to pinpoint the precise conditions to a (un)satisfactory performance in three LC‐MS systems. It is demonstrated that the learned model can be applied to predict LC‐MS system performance for brain samples generated from an independent study. By compiling these predictive models into our web‐application, QCMAP allows users to benchmark the performance of their LC‐MS systems using their own samples and identify key factors for instrument optimization. QCMAP is freely available from: http://shiny.maths.usyd.edu.au/QCMAP/.

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