Microarray software suite

View 1 excerpt, cites methods. Tools for managing and analyzing microarray data. Briefings Bioinform. Micro-Analyzer: Automatic preprocessing of Affymetrix microarray data. Methods Programs Biomed.

Mayday - integrative analytics for expression data. In large-scale transcriptome analysis with DNA microarrays, experimentalists are typically using clustering or pattern recognition algorithms that group genes with similar expression profiles into … Expand.

Clustering microarray data. Methods in enzymology. Guide: a desktop application for analysing gene expression data. BMC Genomics. Computer Tools to Analyze Microarray Data. Methods in molecular biology. TM4 microarray software suite. Create assays tailored directly to specific needs for applications such as targeted region genotyping and fine mapping. It also enables project and data management, lab workflow management, and reporting for Illumina genotyping array experiments.

Access online training to learn how to analyze data with GenomeStudio and Beeline microarray software. Microarray software tools to ensure optimal time-to-answer. Microarray Data Analysis and Experimental Design. Overview of Microarray Software. We have developed a suite of software applications, known as TM4, to support such gene expression studies. The suite consists of open-source tools for data management and reporting, image analysis, normalization and pipeline control, and data mining and visualization.

This chapter describes each component of the suite and includes a sample analysis walk-through. Full text links Read article at publisher's site DOI : Smart citations by scite.

The number of the statements may be higher than the number of citations provided by EuropePMC if one paper cites another multiple times or lower if scite has not yet processed some of the citing articles. Explore citation contexts and check if this article has been supported or disputed.

Similar Articles To arrive at the top five similar articles we use a word-weighted algorithm to compare words from the Title and Abstract of each citation. Bioinformatics analysis of microarray data. Cross-species and cross-platform gene expression studies with the Bioconductor-compliant R package 'annotationTools'. GEPAS, a web-based tool for microarray data analysis and interpretation.

MicroArray Facility: a laboratory information management system with extended support for Nylon based technologies. M IA: a modular open-source application for microarray workflow and integrative datamining.

Analysis of a multifactor microarray study using Partek genomics solution. Pre-processing of microarray data and analysis of differential expression. Joining Europe PMC. Tools Tools overview. ORCID article claiming. Journal list.

Grant finder. Two 2 available segmentation methods histogram and Otsu define the boundaries between each spot and the surrounding local background. Spot intensities are calculated as an integral of non-saturated pixels, although other options including spot median and mean values are available.

Local background subtraction for each reported value is applied by default but can be disabled. The calculated intensities, medians, and means along with each spot position on the array, spot area, background values, and quality control flags are written to a MeV file or the database.

Reusable grid geometry files and automatic grid adjustment allow user to analyze large quantities of images in a consistent and efficient manner. To complement the automated methods, particularly in noisy areas of the slide, the user may manually identify or discard spots. Quality control views allow the user to assess systematic biases in the data. This critical step can help compensate for variability between slides and fluorescent dyes, as well as other systematic sources of error, by appropriately adjusting the measured array intensities.

Data filtering can reduce the dataset by removing poor or questionable data, in addition to data deemed uninteresting or irrelevant to the analysis. MIDAS provides users an intuitive interface to design analysis protocols combining one or more normalization and filtering steps.