DAPAR and ProStaR are software tools to perform the statistical analysis of label-free XIC-based quantitative discovery proteomics experiments. DAPAR contains procedures to filter, normalize, impute missing value, aggregate peptide intensities, perform null hypothesis significance tests and select the most likely differentially abundant proteins with a corresponding false discovery rate. ProStaR is a graphical user interface that allows friendly access to the DAPAR functionalities through a web browser. AVAILABILITY AND IMPLEMENTATION: DAPAR and ProStaR are implemented in the R language and are available on the website of the Bioconductor project (http://www.bioconductor.org/). A complete tutorial and a toy dataset are accompanying the packages. CONTACT: [email protected], [email protected], [email protected].

Genomic data integration is a key goal to be achieved towards large-scale genomic data analysis. This process is very challenging due to the diverse sources of information resulting from genomics experiments. In this work, we review methods designed to combine genomic data recorded from microarray gene expression (MAGE) experiments. It has been acknowledged that the main source of variation between different MAGE datasets is due to the so-called 'batch effects'. The methods reviewed here perform data integration by removing (or more precisely attempting to remove) the unwanted variation associated with batch effects. They are presented in a unified framework together with a wide range of evaluation tools, which are mandatory in assessing the efficiency and the quality of the data integration process. We provide a systematic description of the MAGE data integration methodology together with some basic recommendation to help the users in choosing the appropriate tools to integrate MAGE data for large-scale analysis; and also how to evaluate them from different perspectives in order to quantify their efficiency. All genomic data used in this study for illustration purposes were retrieved from InSilicoDB http://insilico.ulb.ac.be.

The potential of microarray gene expression (MAGE) data is only partially explored due to the limited number of samples in individual studies. This limitation can be surmounted by merging or integrating data sets originating from independent MAGE experiments, which are designed to study the same biological problem. However, this process is hindered by batch effects that are study-dependent and result in random data distortion; therefore numerical transformations are needed to render the integration of different data sets accurate and meaningful. Our contribution in this paper is two-fold. First we propose GENESHIFT, a new nonparametric batch effect removal method based on two key elements from statistics: empirical density estimation and the inner product as a distance measure between two probability density functions; second we introduce a new validation index of batch effect removal methods based on the observation that samples from two independent studies drawn from a same population should exhibit similar probability density functions. We evaluated and compared the GENESHIFT method with four other state-of-the-art methods for batch effect removal: Batch-mean centering, empirical Bayes or COMBAT, distance-weighted discrimination, and cross-platform normalization. Several validation indices providing complementary information about the efficiency of batch effect removal methods have been employed in our validation framework. The results show that none of the methods clearly outperforms the others. More than that, most of the methods used for comparison perform very well with respect to some validation indices while performing very poor with respect to others. GENESHIFT exhibits robust performances and its average rank is the highest among the average ranks of all methods used for comparison.

We present a novel approach for spectral unmixing in hyperspectral imagery called local linear spectral unmixing (LLSU). Our new proposal relies on an existing strategy for non-linear data modelling where a general non-linear model is approximated via several piecewise linear models. The algorithm is the result of hybridizing two well-known strategies for exploratory high-dimensional data analysis: cluster analysis and non-negative matrix factorization. It has been proposed to answer the limitations of global linear unmixing models which are widely used for spectral unmixing. Our strategy is to first group similar pixels from the hyperspctral image via cluster analysis and then to consider a local linear unmixing model for each cluster in order to obtain the constituent endmembers. Subsequently, the resulted local endmembers from each cluster of mixed pixels are at their turn clustered based on their spectral similarity; the final solution is given by the clusters' centroids.

BACKGROUND: With an abundant amount of microarray gene expression data sets available through public repositories, new possibilities lie in combining multiple existing data sets. In this new context, analysis itself is no longer the problem, but retrieving and consistently integrating all this data before delivering it to the wide variety of existing analysis tools becomes the new bottleneck. RESULTS: We present the newly released inSilicoMerging R/Bioconductor package which, together with the earlier released inSilicoDb R/Bioconductor package, allows consistent retrieval, integration and analysis of publicly available microarray gene expression data sets. Inside the inSilicoMerging package a set of five visual and six quantitative validation measures are available as well. CONCLUSIONS: By providing (i) access to uniformly curated and preprocessed data, (ii) a collection of techniques to remove the batch effects between data sets from different sources, and (iii) several validation tools enabling the inspection of the integration process, these packages enable researchers to fully explore the potential of combining gene expression data for downstream analysis. The power of using both packages is demonstrated by programmatically retrieving and integrating gene expression studies from the InSilico DB repository [https://insilicodb.org/app/].

A plenitude of feature selection (FS) methods is available in the literature, most of them rising as a need to analyze data of very high dimension, usually hundreds or thousands of variables. Such data sets are now available in various application areas like combinatorial chemistry, text mining, multivariate imaging, or bioinformatics. As a general accepted rule, these methods are grouped in filters, wrappers, and embedded methods. More recently, a new group of methods has been added in the general framework of FS: ensemble techniques. The focus in this survey is on filter feature selection methods for informative feature discovery in gene expression microarray (GEM) analysis, which is also known as differentially expressed genes (DEGs) discovery, gene prioritization, or biomarker discovery. We present them in a unified framework, using standardized notations in order to reveal their technical details and to highlight their common characteristics as well as their particularities.

Abstract Microarray technology has become an integral part of biomedical research and increasing amounts of datasets become available through public repositories. However, re-use of these datasets is severely hindered by unstructured, missing or incorrect biological samples information; as well as the wide variety of preprocessing methods in use. The inSilicoDb R/Bioconductor package is a command-line front-end to the InSilico DB, a web-based database currently containing 86 104 expert-curated human Affymetrix expression profiles compiled from 1937 GEO repository series. The use of this package builds on the Bioconductor project's focus on reproducibility by enabling a clear workflow in which not only analysis, but also the retrieval of verified data is supported. Availability: inSilicoDb is available as part of the Bioconductor project. There is a companion web interface that can be used for browsing available datasets before importing them into R/Bioconductor (http://insilico.ulb.ac.be). Contact: [email protected]

The clustering capabilities of the Non Negative Matrix Factorization algorithm is studied. The basis images are considered like the membership degree of the data to a particular class. A hard clustering algorithm is easily derived based on these images. This algorithm is applied on a multivariate image to perform image segmentation. The results are compared with those obtained by Fuzzy K-means algorithm and better clustering performances are found for NMF based clustering. We also show that NMF performs well when we deal with uncorrelated clusters but it cannot distinguish correlated clusters. This is an important drawback when we try to use NMF to perform data clustering.

The application of non negative matrix factorization to time series of medical images analyze is investigated in this paper. Time series images of the urinary system are acquired by intravenous pyelography (IVP). Factorial analysis and principal component analysis are often used to extract time signatures or factors and associated compartments of factor images. Blind source separation methods such as independent component analysis (ICA) may be an alternative to these methods for which the orthogonality condition is replaced with a more general constraint: the independence. Since the positivity constraint must not be ignored, we focused on the non negative matrix factorisation approach. More than that, there are situations where only few units of either factor loads and/or factor images are effectively used to represent observed data vectors. In this case, sparseness constraint must be taken into account.

Some clustering algorithms require assumptions (such as number and shape of classes), which limit their performances or provide wrong results. On the contrary, methods based on the estimation of the probability density function (pdf) do not make any assumption neither on the classes shape nor on their number. Two methods based on the pdf, are explored and applied to the segmentation of a multi-spectral image of a cereal grain. The first one is inspired from the estimation of the pdf Parzen-Rosenblatt and the second one estimates the support of the pdf through the support vector theory