May 102015

MIDAS 2.22


MIDAS is one member of a suite of microarray data management and analysis applications developed at The Institute for Genomic Research (J. Craig Venter Institute now).

MIDAS is an application that allows user to perform normalization and other statistical data analysis, trim the raw experimental data, and create output for MeV.

MIDAS is a Java application, provides users an intuitive interface to design analysis protocols combining one or more normalization and filtering steps. In this way, data from many individual hybridizations can be treated in a uniform and reproducible manner. MIDAS reads ?.tav? files generated by TIGR Spotfinder or retrieved from the database via MADAM. Normalization modules include locally weighted linear regression (lowess; (Cleveland and Devlin, 1988; Yang et al., 2002)) and total intensity normalization. These can be linked with filters, including low-intensity cutoff, intensity-dependent Z-score cutoffs, and replicate consistency trimming, creating a highly customizable method for preparing expression data for subsequent comparison and analysis. Data analysis methods are constructed using an intuitive graphical scripting language and can be saved for application to other datasets. MIDAS provides scatterplots that illustrate the effects of each algorithm on the data. When the normalization and filtering steps are complete, MIDAS outputs the data in tav format.


J. Craig Venter Institute



  • Windows/Mac OS X /Linux
  • Java




Referencing MIDAS

Saeed AI, Sharov V, White J, Li J, Liang W, Bhagabati N, Braisted J, Klapa M, Currier T, Thiagarajan M, Sturn A, Snuffin M, Rezantsev A, Popov D, Ryltsov A, Kostukovich E, Borisovsky I, Liu Z, Vinsavich A, Trush V, Quackenbush J. TM4: a free, open-source system for microarray data management and analysis. Biotechniques. 2003 Feb;34(2):374-8.


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