11.2.5 Results
Results are displayed as a Diff Expression annotation track on the reference sequence, colored by the property Differential Expression Confidence. To change the annotation coloring, click the arrow to the left of the track name and choose Color by / Heatmap. For example, you may prefer to color by Differential Expression Log2 Ratio once you have filtered at an appropriate confidence level (e.g using an abs > 6 filter).
The results may be exported as a table in *.csv format from the Annotations tab above the sequence viewer. Click the Track button and choose the Expression track to display. Then click the Columns button and add the results columns you wish to display. Use the Export table button to export the displayed values.
For both the DESeq2 and Geneious methods, each Expression Difference annotation produced will have the following properties:
- Differential Expression p-value: A p-value indicating the confidence that this gene is differentially expressed.
- Differential Expression adjusted p-value (DESeq2 results only): The p-value adjusted for multiple tests.
- Differential Expression Absolute Confidence: The negative base 10 logarithm of the p-value (adjusted p value for DESeq2 results). This field is useful for filtering on. For example in the Filter box on the results, you could type “absolute confidence>6” (without quotes) to only show genes that we are fairly confident have differential expression. Since filtering works on partial property names, in most cases just a shorter filter like abs > 6 is sufficient unless your genes have existing numeric properties containing the text “abs”.
- Differential Expression Confidence: The same as Absolute Confidence, but adjusted to be negative for genes that are under expressed in sample 2 compared to sample 1, or positive for over expressed genes. The results are colored based on this property, from blue for under expressed genes, through to white for genes that are not differentially expressed, through to red for genes that are over expressed. Confidence coloring reaches maximum intensity at ± 8.
- Differential Expression Ratio: (Geneious method only) The ratio of the normalized values between the two samples, but ratios less than one are replaced with −value−1. This results in a value greater than 1 for over expressed genes and less than −1 for under expressed genes. When one sample has no or very low expression, the ratio is capped at ± 1,000,000. Ratio coloring reaches maximum intensity at ± 5.
- Differential Expression Log2 Ratio: The base 2 log of the ratio of the normalized values between the two samples. When one sample has no or very low expression, the log2 ratio is capped at ± 1,000,000.