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Data on features - genes, transcripts, and exons - is presented before and after normalization as _reads and _rpkm spreadsheets. In these spreadsheets, samples are listed one per row and the normalized counts of the reads mapped to features are in columns. _rpkm spreadsheets can be used to perform differential expression analysis using ANOVA. It may also be useful to view how samples group together using a PCA plot. Select View > Scatter Plot from the toolbar or press Image Removed Image Added on the quick action bar to create a PCA plot from the selected spreadsheet. For more information about an example of using PCA plots, see Exploratory Gene Expression Data Analysis or consult Chapter 7 of the Partek User's Manual for a detailed introduction to PCA. With replicates, you would also be able to perform Differential expression analysis using ANOVA.