I'm trying out the new ANCOVA tool. Two questions/issues: 1) where do I enter/indicate my covariates? 2) Whenever I run it I get the error message: "The gene annotation you have selected does not match the annotation in the gene sets." This happens regardless of whether I use my dataset (with or without my covariates in the dataset-Affymetrix U133 2.0) or the practice dataset for Affymetrix (the U133 plus 2), and regardless of what annotation I choose in the ANCOVA window (I'm downloading from GenesigDB). Thanks!
The covariates are entered using the button selection tool or the cluster selector if you have made clusters. The error message you are receiving is shown when the gene set file you are using does not match up with the annotation type that you have selected. Have you checked to see that annotation has been properly loaded?
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