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 The zipped project file contains several prepared files used in this analysis as well as the annotation information for the BeadChip. The zipped file also contains a Partek project file (.ppj).

• After downloading the file, go to File > Import > Zipped project... and browse to GO_Enrichment.zip on your local drive

Partek Genomics Suite will automatically unzip the file, read the .ppj file, open and annotate all spreadsheets (Figure 1). The parent spreadsheet (GSE8479-AVGSignal) contains the original intensity data. The first child spreadsheet (ANOVAResults) contains the results of differential gene expression analysis from a 3-way ANOVA. The second child spreadsheet (Gene_List.txt) is a list of significantly differentially expressed genes. When working with your own data, you will need to detect differentially expressed genes and create a gene list yourself.