Analysis of microarray data - VSN International

Analysis of Microarray Data in GenStat 65Affymetrix microarray exampleArabidopis is a simple plant often used in gene studies. Affymetrix Arabidopis chips (ATH1-121501)have 22810 probe sets arranged in a 712 x 712 grid. In this experiment, nine of these chips (slides) wereused. The CEL file data for these chips are stored in the files hyb1191.CEL-hyb11400.CEL that can befound in the Microarrays folder (see page 2). The layout of probes and quality control units (not used inthe analysis) can be found in the CDF file ATH1-121501B.CDF. The nine slides have three replicates ofthree targets applied to them.To calculate expression values for these slides,open them with the Stats | Microarrays | Data |Affymetrix CEL files menu item as shown top theright.Now select the CEL files by using the Browsebutton as shown below.Select the nine CEL files as shown to the right.Click the Browse button by the CDF file entryto select the CDF file as shown below.You may need to use the Up and Down buttons tomove a selected CEL files to the correct location in thelist. The order the files end up in the list depends onhow they are selected in the open dialog, but Windowsdoes not always seem to give a logical ordering tothese. This should give you the completed menu to theright.