DNA Microarray Analysis Tools
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  1. ArrayQuest™ is a web-based program for the analysis of DNA microarray data. ArrayQuest™ is designed to apply various types of Open Source analysis scripts (i.e., Bioconductor analysis methods) to microarray data held in the MUSC DNA Microarray Database and NIH GEO or data uploaded to the system.

  2. dChip DNA-Chip Analyzer is a software package implementing model-based expression analysis of oligonucleotide arrays (Li and Wong 2001) and several high-level analysis procedures. This software is well suited for the analysis of Affymetrics GeneChips and can be licensed freely by academic users. For a given set of samples, dChip selects the chip with median overall brightness to normalize all other arrays. A subset of Perfect Match (PM) probes with small within-subset rank difference in the two arrays is used as a basis for the normalization (Invariant Set Normalization). For more information on the smoothing process involved in Invariant Set Normalization, please refer to Li and Wong 2001.

  3. GeneSifter.Net is a Web-based microarray analysis system that combines data management and analytical functions with current gene annotations from databases such as UniGene and LocusLink.

  4. BRB ArrayTools is an integrated package for the visualization and statistical analysis of DNA microarray gene expression data.




The MUSC DNA Microarray and Bioinformatics Facility is supported by grants from the National Cancer Institute (R24CA095841) and the National Heart Lung and Blood Institute (P20RR016434) as well as funds from the University Research Resource Foundation. µArrayDB™ (© 2002) is a product of ProSoft Systems.