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The result will be displayed in a child spreadsheet, ANOVA-3way (ANOVAResults). In this spreadsheet, each row represents a gene probe set and the columns represent the computation results for that gene probe set (Figure 4).  By Although not synonymous, probe set and gene will be treated as synonyms in this tutorial for convenience. By default, the genes are sorted in ascending order by the p-value of the first categorical factor. In this tutorial,Type is the first categorical factor, which means the most highly significant differently expressed gene between Down syndrome and normal samples is at the top of the spreadsheet in row 1.

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You basically identify genes with probesets. Although this is convenient and straightforward, it is not actually true. Perhaps a sentence explaining that for convenience these terms will be treated as synonims, although...

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Generate these plots for rows 3 (DSCR3) and 8 (CSTB). If the lines in the interaction plot are not parallel, then there is a chance that there is an interaction between Tissue and Type. Error bars show standard error of the least squared mean. DSCR3 is a good example of this (Figure 7). We can look at the p-values in column 9, p-value(Type * Tissue) to check if this apparent interaction is statistically significant. 

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We can view the expression levels of a gene for each sample using a dot plot.

• Right click on the gene row header and select Dot Plot (Orig. Data) from the pop-up menu. This generates a Dot Plot tab for the selected gene (Figure 8)
  
  

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