Raw data files can be downloaded individually from the "Samples and Data" page in the rightmost column (Figure 16). For microarray experiments, a zipped archive file can be downloaded from the "Experiment" page (Figure 16), which contains all raw data files belonging to the study. Sometimes multiple zip files are created to keep the downloadable files below 200 MB.
Figure 16 Where to find links to download raw/processed data files.
The types of raw data files vary depending on the platform (array manufacturer or sequencing machine). For Affymetrix microarrays, CEL files are common, while Agilent arrays often generate tab-delimited text matrices. Most sequencing-based experiments provide FASTQ files, containing raw sequence reads.
We will look more at the different data types in the next section.