Analysis of Microarray Results
Effective analysis of microrarray data is an ongoing challenge. The UC Davis Genome Center is attempting to address this need through services provided by the Bioinformatics Core. The core director is Dawei Lin (lhslin@ucdavis.edu) and he is in the process of setting up analytical and educational resources to enable the campus community (and others) to derive useful information from the vast amount of data generated in every microarray experiment. Dr. Lin is always interested in hearing from researchers about what services they feel would be most valuable so please don't hesitate to contact him.
In regards to the Illumina expression platform data, there are different analysis options. Packages in Bioconductor have been written that work with the raw array tiff file and location files (eg, see http://www.bioconductor.org/packages/bioc/1.8/html/beadarray.html). Data files in the appropriate format are provided to you, so if you're familiar with R/bioconductor you're all set. The Bead Studio software itself permits some analysis options. As part of the service fee, basic instruction on the software is provided. Access to the software is available on facility workstations. For more information on the normalization and other analytical options provided in the Illumina package, consult this document.
ChIP-chip data generated on Nimblegen or other platforms requires specific software, separate from packages used to analyze gene expression data. For NimbleGen arrays, we provide access to the manufacturer's software used to analyze their arrays (NimbleScan 2.4 and Signal Map 1.8). Access to programs written in the Farnham lab to identify peaks in promoter or tiling arrays can be found on the lab's home page. These programs are written in perl and can be distributed, however, when used they must be specifically cited. Details will be provided.
In addition, many microarray analysis software utilities are available as open source downloads, and below are some places to begin explorations of these programs.
Software Resources
R and Bioconductor: Bioconductor is an open source and open development software project for the analysis and comprehension of genomic data using the R statistical package. From this site you can access R, the bioconductor analytic packages, and get additional information and documentation.
NextBio: As described on their web page, NextBio is a life science search engine that enables researchers and clinicians to access and understand the world's life sciences information. NextBio is open biology — search across all of the world's life science information, share data, and collaborate. The UCD Mind Institute currently utilizes NextBio resources.
Microarrays: A public resource created and maintained by the DeRisi lab at UCSF, for microarray protocols and software. Many good links within.
BRB Array Tools An integrated package for the visualization and statistical analysis of DNA microarray gene expression data.
DAVID and EASE Free NCBI software for the annotation and analysis of genome-scale datasets derived from high-throughput technologies such as microarray and proteomic platforms.
MIAME This site describes the Minimum Information About a Microarray Experiment that is needed to enable the interpretation of the results of the experiment unambiguously and potentially to reproduce the experiment; most journals will require data to be submitted in this format.