MOTIVATION: The identification and discovery of phenotypes from high content screening images is a challenging task. Earlier works use image analysis pipelines to extract biological features, supervised training methods or generate features with neural networks pretrained on non-cellular images. We introduce a novel unsupervised deep learning algorithm to cluster cellular images with similar Mode-of-Action (MOA) together using only the images' pixel intensity values as input. It corrects for batch effect during training. Importantly, our method does not require the extraction of cell candidates and works from the entire images directly. RESULTS: The method achieves competitive results on the labeled subset of the BBBC021 dataset with an accuracy of 97.09% for correctly classifying the MOA by nearest neighbors matching. Importantly, we can train our approach on unannotated datasets. Therefore, our method can discover novel MOAs and annotate unlabeled compounds. The ability to train end-to-end on the full resolution images makes our method easy to apply and allows it to further distinguish treatments by their effect on proliferation. AVAILABILITY AND IMPLEMENTATION: Our code is available at https://github.com/Novartis/UMM-Discovery. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Cell autonomous cancer dependencies are now routinely identified using CRISPR loss-of-function viability screens. However, a bias exists that makes it difficult to assess the true essentiality of genes located in amplicons, since the entire amplified region can exhibit lethal scores. These false-positive hits can either be discarded from further analysis, which in cancer models can represent a significant number of hits, or methods can be developed to rescue the true-positives within amplified regions. We propose two methods to rescue true positive hits in amplified regions by correcting for this copy number artefact. The Local Drop Out (LDO) method uses the relative lethality scores within genomic regions to assess true essentiality and does not require additional orthogonal data (e.g. copy number value). LDO is meant to be used in screens covering a dense region of the genome (e.g. a whole chromosome or the whole genome). The General Additive Model (GAM) method models the screening data as a function of the known copy number values and removes the systematic effect from the measured lethality. GAM does not require the same density as LDO, but does require prior knowledge of the copy number values. Both methods have been developed with single sample experiments in mind so that the correction can be applied even in smaller screens. Here we demonstrate the efficacy of both methods at removing the copy number effect and rescuing hits from some of the amplified regions. We estimate a 70-80% decrease of false positive hits with either method in regions of high copy number compared to no correction.

SUMMARY: The assessment of data quality is a major concern in microarray analysis. arrayQualityMetrics is a Bioconductor package that provides a report with diagnostic plots for one or two colour microarray data. The quality metrics assess reproducibility, identify apparent outlier arrays and compute measures of signal-to-noise ratio. The tool handles most current microarray technologies and is amenable to use in automated analysis pipelines or for automatic report generation, as well as for use by individuals. The diagnosis of quality remains, in principle, a context-dependent judgement, but our tool provides powerful, automated, objective and comprehensive instruments on which to base a decision. AVAILABILITY: arrayQualityMetrics is a free and open source package, under LGPL license, available from the Bioconductor project at www.bioconductor.org. A users guide and examples are provided with the package. Some examples of HTML reports generated by arrayQualityMetrics can be found at http://www.microarray-quality.org

Abstract Summary:ArrayExpress is one of the largest public repositories of microarray datasets. R/Bioconductor provides a comprehensive suite of microarray analysis and integrative bioinformatics software. However, easy ways for importing datasets from ArrayExpress into R/Bioconductor have been lacking. Here, we present such a tool that is suitable for both interactive and automated use. Availability: The ArrayExpress package is available from the Bioconductor project at http://www.bioconductor.org. A users guide and examples are provided with the package. Contact: [email protected] Supplementary information: Supplementary data are available Bioinformatics online.