SUMMARY: Whole-genome microarrays allow us to interrogate the entire transcriptome of a cell. Affymetrix microarrays are constructed using several probes that match to different regions of a gene and a summarization step reduces this complexity into a single value, representing the expression level of the gene or the expression level of an exon in the case of exon arrays. However, this simplification eliminates information that might be useful when focusing on specific genes of interest. To address these limitations, we present a software package for the R platform that allows detailed analysis of expression at the probe level. The package matches the probe sequences against a target gene sequence (either mRNA or DNA) and shows the expression levels of each probe along the gene. It also features functions to fit a linear regression based on several genetic models that enables study of the relationship between gene expression and genotype. AVAILABILITY AND IMPLEMENTATION: The software is implemented as a platform-independent R package available through the Bioconductor repository at http://www.bioconductor.org/. It is licensed as GPL 2.0. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

UNLABELLED: Infectious diseases are a major threat to global public health and prosperity. The causative agents consist of a suite of pathogens, ranging from bacteria to viruses, including fungi, helminthes and protozoa. Although these organisms are extremely varied in their biological structure and interactions with the host, they share similar methods of evading the host immune system. Antigenic variation and drift are mechanisms by which pathogens change their exposed epitopes while maintaining protein function. Accordingly, these traits enable pathogens to establish chronic infections in the host. The varDB database was developed to serve as a central repository of protein and nucleotide sequences as well as associated features (e.g. field isolate data, clinical parameters, etc.) involved in antigenic variation. The data currently contained in varDB were mined from GenBank as well as multiple specialized data repositories (e.g. PlasmoDB, GiardiaDB). Family members and ortholog groups were identified using a hierarchical search strategy, including literature/author-based searches and HMM profiles. Included in the current release are>29,00 sequences from 39 gene families from 25 different pathogens. This resource will enable researchers to compare antigenic variation within and across taxa with the goal of identifying common mechanisms of pathogenicity to assist in the fight against a range of devastating diseases. AVAILABILITY: varDB is freely accessible at http://www.vardb.org/

MOTIVATION: Microarray-based expression profiles have become a standard methodology in any high-throughput analysis. Several commercial platforms are available, each with its strengths and weaknesses. The R platform for statistical analysis and graphics is a powerful environment for the analysis of microarray data, because it has many integrated statistical methods available as well as the specialized microarray analysis project Bioconductor. Many packages have been added in the last few years increasing the range of possible analysis. Here, we report the availability of a package for reading and analyzing data from GE Healthcare Gene Expression Bioarrays within the R environment. AVAILABILITY: The software is implemented in the R language, is open source and available for download free of charge through the Bioconductor (http://www.bioconductor.org) project.