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Selecting Affymetrix probesets using Jetset or collapse
Qlucore Omics Explorer
Date Created
2014-10-15 14:32:34
Date Updated
2014-10-15 14:58:09
There are multiple probe sets matching a gene in a normal Affymetrix array and sometimes a unique measurements for each gene is required. How should this be done?
There can be many approaches to this.

One option is to use the inbuilt collapse (data tab) function in Qlucore Omics Explorer. Four methods are supported; mean, median, min and max.

Another option is to use a quality score to do the selection. One published approach is Jetset. Jetset: selecting an optimal microarray probe set to represent a gene Qiyuan Li, Nicolai J. Birkbak, Balazs Gyorffy, Zoltan Szallasi, and Aron C. Eklund. BMC Bioinformatics 2011, 12:474.

If you use Jetset the workflow would like this.
1. Download and unzip the Jetset file for the array you are using.
2. Start Qlucore Omics Explorer. Select File | Import | Variable annotations (make sure the file filter shows all files to see the *.csv file)
3. Select to import the "Best" column only
4. Press the Search icon in the Variable tab. Search the "Best" annotation using text setting and equal for the value TRUE. This will give you a Search list with all the probe sets that are regarded as best by Jetset.
5. Copy the Search list and give the new list a descriptive name
6. Select to use the new list as the base by pressing the checkbox in front of the list in the variable panel.
7. You can now continue the analysis with only the "Best" probe sets.

To avoid going through these steps each time you are working with this data set, save a copy using File and Save as.
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