## Frequently asked questions about Class Scoring

- The resampling is taking too long, any suggestions?

  Answer: There are few ways to speed things up. One is to not look at very large values for the "maximum class size" value. We usually use a value near 200. Another is to reduce the number of iterations. You might try temporarily setting this to 10000 while you experiment with the other settings, and then, once you find a setting you like, you can crank up the iterations for the "final" run (for example to 200000, which still should not take very long).

- Do I input the list of gene scores for the significantly changed genes, or all the genes?

  Answer: All of them. The resampling method uses the gene scores for all the genes. The built-in overrepresentation analysis will use the threshold you set in the "ORA score threshold" parameter to select genes. Note that we find that removing unexpressed genes can help the analysis, but it isn't required.

- When I open the output file in Notepad it looks like a mess of letters and numbers.

  Answer: The output will not look right when viewed in a text editor or a web browser. It will look correct in Excel if you open it as a tab delimited file.

- I don't see annotation file for my microarray. What should I do?

  Answer: Unfortunately we cannot generally create annotations for microarrays that are not commonly used. If we identify a commonly used platform, we will add it. This means that 'home made' spotted microarrays are not supported in most cases. Feel free to let us know if you have a microarray design that needs annotations for class scoring.

- There are mistakes in the Gene Ontology annotations.

  Answer: We download the annotations from public sources and are not responsible for any errors. We normally update our annotations every two months. Note that we use as many annotations as we can get, which means we use the 'IEA' annotations.

- Which options should I use?

  Answer: We routinely use the "mean" class score method, with the "best" replicate scoring, with 200,000 iterations. However, we provide several options to allow users to experiment with what gives them the most interesting results.

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