Help:How do I download microarray data

From VectorBase Help System

[edit] Statistical summary data

Now available from the downloads page for Anopheles gambiae only at present, there are tab-delimited files of gene-averaged expression summary data. These are the p-values and text summaries you can find on the web with URLs taking the form http://funcgen.vectorbase.org/ExpressionData/gene/XYZ (where XYZ is the gene ID or symbol).

Coming soon we will have reporter-averaged expression data available from BioMart. This will allow advanced data query and retrieval, with the option to link queries to the gene set data.

[edit] Processed data

By processed data we mean:

• for two-colour data, either background subtracted median intensities, or lowess normalised background subtracted median intensities.
• for Affymetrix data, the RMA expression values

You can download processed microarray data for an entire experiment as follows:

1. Log in to the VectorBase BASE server as 'vbguest' following on-screen instructions
2. Click view→experiments then select "all" from the --view/presets-- menu.
3. When you see a list of experiments, click on the "Analyze" link next to the one you are interested in.
4. Then click the "Export data" icon to the right of the analysis step you wish to download.
5. Follow the instructions on screen (you must leave the "save as" name blank to trigger an immediate download, it will not work otherwise). MEV format is recommended.

You can also find the raw data files in the BASE server, look for the "Raw bioassays" associated with each experiment.

[edit] Raw data

By raw data we mean the files that were provided by the data submitter. These usually come straight from the image analysis software (e.g. GenePix).

1. Log in to the VectorBase BASE server as 'vbguest' following on-screen instructions
2. Click view→experiments then select "all" from the --view/presets-- menu.
3. Click on the experiment name of interest.
4. Click on any one of the "raw bioassays" listed for the experiment
5. Click on the filename for the raw data file (either "CEL file" or "Generic raw data")
6. We would now like to see all the files in the same directory as this file, but there is a small bug in BASE which makes this counterintuitive to achieve. Click on the highlighted directory in the left-hand panel tree view of the file browser. Nothing happens (unless the bug has been fixed and we forgot to change these instructions). You have to click on another directory and then back to the one which was highlighted. Then you get a full listing of that directory.
7. Use the checkboxes to select all the files you wish to download
8. Click on the "Export" button above the file list
9. Select the archive format you wish to use (zip, tar etc), click "Next"
10. Click on the "Save as" item, and erase the filename text to the right. As the on-screen help text explains, this will cause an immediate download (rather than create a new file on the server, which you don't have permission to do as "vbguest").
11. Click "Next" and follow all on-screen instructions carefully to download the file to your computer

If the raw data filenames are not self-explanatory, you should contact the VectorBase help desk to request a tab-delimited text file describing the hybridisations. There is currently no way to do this automatically in BASE. Alternatively, if you cannot wait, you can click on each "raw bioassay", make a note of the raw data filename, then click on the "Annotations and parameters" tab to see the sample characteristics.