Micro-array Analysis
From BITS wiki
Microarrays generated high-throughput data which requires specific knowledge of statistics and the samples used in the experiment to obtain relevant results.
Contents
Microarray providers
The Nucleomics Core of the VIB can help you reaching your goal in microarray analysis.
Microarray data databases
It is obligatory for dissemination of scientific results to set free your data. Here links to repositories for microarray data are gathered.
General
- GEO (Gene Expression Omnibus) - NCBI database on microarray data.
- ArrayExpress - EBI database on microarray data
- InsilicoDb - Curated microarray datasets ready to import into different tools.
Bacteria specific
- Many Microbes Microarray Database - webtools for array analysis included
- Escherichia coli microarray data
- E. coli Gene Expression Database of O.U. - Contains a lot of visualisation tools. More information on using this tool [4]
Microarray file formats
see also here.
- General file formats
- .soft - The Simple Omnibus Format in Text (from GEO website)
- Affymetrix associated file formats
- .cel - File from Affymetrix chip, containing raw data with spot information
- .gpr - File from the GenePix program
- .chp -
- .clf - Cell layout file that maps probe IDs to a location (x- and y-coordinates) in the CEL file.
- .bgp - Background probe file that lists the probes to use for background correction.
- .cdf - Library file containing information about which probes belong to which probe set.
- .gin - Library file containing information about the probe sets, such as the gene name associated with the probe set.
- Sample data from Affymetrix
Microarray data analysis tools
- RStudio in combination with Bioconductor packages - very powerful and flexible, requires coding, and a lot of digging into manuals not always of high quality.
- oneChannelGUI, a bioconductor package, providing an graphical user interface that removes the necessity to type commands.
- GenMAPP - allows you to display your expression information to pathways - free online. See the short but very good introduction here!
- GEPAS - A complete analysis suite for microarray data analysis - free online. Has a very good documentation and tutorials section.
- GenePattern - online, by the Broad Institute.
- MayDay - downloadable JAVA
- TM4 - a very popular microarray data analysis software package (formerly TIGR, now maintained at the Dana-Farder Cancer Institute).
- Babelomics - A powerfull online portal for MA analysis up to network enrichment
- BRB Array Tools -
Statistics
- Poweratlas - Estimate the power of experiments based on comparison
Additional information
- This page gives you a good introductionary overview of the different steps in MA analysis and the detection of significantly differentially expressed genes.
- Extensive list of all public domain tools
- Commercial software catalogue for MA analysis
