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.