Microarray experiments

Array manufacturers often provide software to open and analyse their raw data files (Table 1). These programs may not always be available or may not be flexible enough for your needs. There are several free software tools that are suitable for the downstream processing of microarray files. Examples include the Galaxy platform (10), GenePattern (11) and the statistics software R (12).

Manufacturer Typical raw data format How to open / Analysis software examples

Affymetrix

.CEL R packages (affy, limma, oligo...)
Agilent feature extraction file (tab-delimited text file per hybridisation) Spreadsheet software (Excel, OpenOffice, etc.)
GenePix (scanner) .gpr (tab-delimited text file per hybridisation) Spreadsheet software (Excel, OpenOffice, etc.)
Illumina .idat R packages (e.g. illuminaio)
Illumina txt (tab-delimited text matrix for all samples) Spreadsheet software (Excel, OpenOffice, etc.)
Nimblegen NimbleScan, pair (tab-delimited text matrix for all samples) Spreadsheet software (Excel, OpenOffice, etc.)

Table 1 Common microarray raw data file types.