MultiBaC: an R package to remove batch effects in multi-omic experiments.

MOTIVATION: Batch effects in omics datasets are usually a source of technical noise that masks the biological signal and hampers data analysis. Batch effect removal has been widely addressed for individual omics technologies. However, multi-omic datasets may combine data obtained in different batches where omics type and batch are often confounded. Moreover, systematic biases may be introduced without notice during data acquisition, which creates a hidden batch effect. Current methods fail to address batch effect correction in these cases. RESULTS: In this article, we introduce the MultiBaC R package, a tool for batch effect removal in multi-omics and hidden batch effect scenarios. The package includes a diversity of graphical outputs for model validation and assessment of the batch effect correction. AVAILABILITY AND IMPLEMENTATION: MultiBaC package is available on Bioconductor (https://www.bioconductor.org/packages/release/bioc/html/MultiBaC.html) and GitHub (https://github.com/ConesaLab/MultiBaC.git). The data underlying this article are available in Gene Expression Omnibus repository (accession numbers GSE11521, GSE1002, GSE56622 and GSE43747). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

MultiBaC: A strategy to remove batch effects between different omic data types.

Diversity of omic technologies has expanded in the last years together with the number of omic data integration strategies. However, multiomic data generation is costly, and many research groups cannot afford research projects where many different omic techniques are generated, at least at the same time. As most researchers share their data in public repositories, different omic datasets of the same biological system obtained at different labs can be combined to construct a multiomic study. However, data obtained at different labs or moments in time are typically subjected to batch effects that need to be removed for successful data integration. While there are methods to correct batch effects on the same data types obtained in different studies, they cannot be applied to correct lab or batch effects across omics. This impairs multiomic meta-analysis. Fortunately, in many cases, at least one omics platform-i.e. gene expression- is repeatedly measured across labs, together with the additional omic modalities that are specific to each study. This creates an opportunity for batch analysis. We have developed MultiBaC (multiomic Multiomics Batch-effect Correction correction), a strategy to correct batch effects from multiomic datasets distributed across different labs or data acquisition events. Our strategy is based on the existence of at least one shared data type which allows data prediction across omics. We validate this approach both on simulated data and on a case where the multiomic design is fully shared by two labs, hence batch effect correction within the same omic modality using traditional methods can be compared with the MultiBaC correction across data types. Finally, we apply MultiBaC to a true multiomic data integration problem to show that we are able to improve the detection of meaningful biological effects.

NIR hyperspectral imaging to evaluate degradation in captopril commercial tablets.

Pharmaceutical quality control is important for improving the effectiveness, purity and safety of drugs, as well as for the prevention or control of drug degradation. In the present work, near infrared hyperspectral images (HSI-NIR) of tablets with different expiration dates were employed to evaluate the degradation of captopril into captopril disulfide in different layers, on the top and on the bottom surfaces of the tablets. Multivariate curve resolution (MCR) models were used to extract the concentration distribution maps from the hyperspectral images. Afterward, multivariate image techniques were applied to the concentration distribution maps (CDMs), to extract features and build models relating the main characteristics of the images to their corresponding manufacturing dates. Resolution methods followed by extracting features were able to estimate the tablet manufacture date with a prediction error of 120days. The model developed could be useful to evaluate whether a sample shows a degradation pattern consistent with the date of manufacturing or to detect abnormal behaviors in the natural degradation process of the sample. The information provided by the HIS-NIR is important for the development of the process (QbD), looking inside the formulation, revealing the behavior of the active pharmaceutical ingredient (API) during the product's shelf life.

Assessment of cluster yield components by image analysis.

BACKGROUND: Berry weight, berry number and cluster weight are key parameters for yield estimation for wine and tablegrape industry. Current yield prediction methods are destructive, labour-demanding and time-consuming. In this work, a new methodology, based on image analysis was developed to determine cluster yield components in a fast and inexpensive way. RESULTS: Clusters of seven different red varieties of grapevine (Vitis vinifera L.) were photographed under laboratory conditions and their cluster yield components manually determined after image acquisition. Two algorithms based on the Canny and the logarithmic image processing approaches were tested to find the contours of the berries in the images prior to berry detection performed by means of the Hough Transform. Results were obtained in two ways: by analysing either a single image of the cluster or using four images per cluster from different orientations. The best results (R(2) between 69% and 95% in berry detection and between 65% and 97% in cluster weight estimation) were achieved using four images and the Canny algorithm. The model's capability based on image analysis to predict berry weight was 84%. CONCLUSION: The new and low-cost methodology presented here enabled the assessment of cluster yield components, saving time and providing inexpensive information in comparison with current manual methods.

Near infrared hyperspectral imaging for forensic analysis of document forgery.

Hyperspectral images in the near infrared range (HSI-NIR) were evaluated as a nondestructive method to detect fraud in documents. Three different types of typical forgeries were simulated by (a) obliterating text, (b) adding text and (c) approaching the crossing lines problem. The simulated samples were imaged in the range of 928-2524 nm with spectral and spatial resolutions of 6.3 nm and 10 µm, respectively. After data pre-processing, different chemometric techniques were evaluated for each type of forgery. Principal component analysis (PCA) was performed to elucidate the first two types of adulteration, (a) and (b). Moreover, Multivariate Curve Resolution-Alternating Least Squares (MCR-ALS) was used in an attempt to improve the results of the type (a) obliteration and type (b) adding text problems. Finally, MCR-ALS and Partial Least Squares-Discriminant Analysis (PLS-DA), employed as a variable selection tool, were used to study the type (c) forgeries, i.e. crossing lines problem. Type (a) forgeries (obliterating text) were successfully identified in 43% of the samples using both the chemometric methods (PCA and MCR-ALS). Type (b) forgeries (adding text) were successfully identified in 82% of the samples using both the methods (PCA and MCR-ALS). Finally, type (c) forgeries (crossing lines) were successfully identified in 85% of the samples. The results demonstrate the potential of HSI-NIR associated with chemometric tools to support document forgery identification.