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The _reads and _rpkm spreadsheets can be used for data analysis. Sample grouping can be visualized using PCA. Select View > Scatter Plot from the toolbar or press  on the quick action bar to create a PCA plot from the selected spreadsheet. See Exploring Gene Expression Datagene expression data for an example of using PCA plots for data analysis or consult Chapter 7 of the Partek User's Manual for a detailed introduction to PCA. With replicates in a sample group, you would also be able to use the _rpkm spreadsheet to perform differential expression analysis using ANOVA. 

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The contents of this spreadsheet are explained in more detail in a later section of the tutorial - Detecting Unexplained Regions. 

References

Mortazavi, A., Williams, B.A., McCue, K., Schaeffer, L., & Wold, B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature, 2008; 5: 621-8.

Xing Y, Yu T, Wu YN, Roy M, Kim J, Lee C: An expectation-maximization algorithm for probalisitic reconstructions of full-length isoforms from splice graphs. Nucleic Acids Res 2006, 34: 3150-3160. 

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