Affymetrix Data

To link the affymetrix files to the array images (  ), click on each array and set the affymetrix data and image files by clicking the Load Experiment(    ) buttons in the Data Tab. Set the CDF File. If you need to do normalizations or present your results as log ratios, select one of your arrays to use as Base.

Decide whether you want your result presented as Log ratio or Absolute values

It is now a good idea to save the experiment. Save by clicking the Save Experiment(    ) button, to the left of the divider, underneath the experimental design.

Quality Control

The    Quality Control button opens a window that allows you to examine the quality of your chip. All statistics used on probe pairs and probe sets are taken from http://www.affymetrix.com/support/technical/whitepapers/sadd_whitepaper.pdf

The table shown in this window displays information on each probe pair in your dataset. A probe pair consists of two probes, one that matches perfectly to the target mRNA (PM) and a probe where one mismatch (MM) has been introduced.

Each row has information on a probe set. A probe set is a collection of probe pairs, all with the same mRNA as a target, located at different places around the array. Ideally all PM probes within one probe set and all MM probes should have the same intensity, or at least similar ratios of each probe pair. This is often not the case.

The table values can be presented in three different ways:

• Chart - each row has a graph area, where a red dash is drawn for each PM and a blue dash for each MM. High intensities are drawn near the ceiling of the row, low intensities near the floor of the row.
• Values - the absolute intensity values
• Log cells - displays the affymetrix scanned cells. These are in a shade of grey. A black square means no intensity, a white square means maximum intensity.

The probe that has a mismatch introduced into it, should have lower intensity than its PM variant. If the MM probe has higher intensity than the PM probe, an ideal mismatch (IM) is calculated. To view the calculated ideal mismatches click the IM button. Click forth and back between MM and IM buttons to see where an ideal mismatch has been calculated.

If you are looking for particular probes, you can search for them using a regular expression in the search field provided.