This function uses log2(ratio) to compare and identify regions of difference between two tracks, or two groups of tracks. When working with two groups of tracks, average value of each group will be used to compute ratio.
At control panel, go to "Statistiscs & analysis" → "Pairwise comparison" to find its interface:
Both groups must be assigned with at least one track for each. Click button inside a group box and the heatmap track selection panel is displayed prompting you to make selection:
Click track name in the box to assign them to group:
More conveniently, you can right-click on track in genome heatmap or metadata color map and use menu option to make assignment:
Click number "1" or "2" to assign tracks to that group. Please note that this option will only be visible when the pairwise comparison control panel is open.
To clear track assignment for a group, click the "clear" button of that group.
Once you're done with track selection, click "Run" button and run the pairwise comparison. In the example below, comparison was set on the ChIP-Seq tracks of two histone marks, (H3K27me3 in red as group 1, H3K36me3 in green as group 2) over some blood and immune cell samples from Roadmap Epigenomics Project. In the pairwise comparison track, red bars represent values higher in group 1 (H3K27me3 tracks), green bars represent values higher in group 2 (H3K36me3 tracks):
In case of zero values of either group 1 or 2, log ratio cannot be computed. Instead of colored bars, gray bars are plotted to indicate such cases. Up-pointing gray bar indicates the group 1 value is zero (log value is infinity), down-pointing gray bar indicates the group 2 value is zero (log value is -infinity). If values from both groups are zero, no bars will be plotted.
Right click on log-ratio track to yield context menu:
To configure track rendering, select wrench option. Following panel will appear in floating toolbox:
Click color blobs to change the two bar colors:
And use radio boxes to change the method of defining Y axis. Details are available in chapter of genome heatmap tracks. Keep in mind the scale configuration is based on log-transformed value, not original ratio.
In context menu on log-ratio track, select "Bird's eye view" option:
The genome-wide pairwise comparison will be displayed in Bird's Eye View panel:
Please refer to chapter of Bird's Eye View for details.
Last modifed: 1/3/2012