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Example 2way plot

Create 2way plots that show the relationships between gene (or RNA processing event) levels in two different samples. The x-axis will correspond to one sample, and the y-axis to another. The pair of samples (or groups of samples) must be a comparison pre-specified in comps.txt. Points will correspond to genes (or RNA processing events, e.g. cassette exons), and be colored according to whether they are significantly different in the two samples, and whether they are up or down. The numbers of up and down genes or events will also be displayed.

After the plot is created, action buttons are presented to the user to access the significantly changed genes or RNA processing events in the table browser.

2way Options
Comparison Three drop-down menus, which must be selected in order:
  1. Project
  2. Comparison (named comparison from comps.txt) for that project
  3. Event type: for example "genes" or "skipped exons".
P P-value cutoff for significance. Usually 1e-4 is used, as this roughly corresponds to 1-3 expected false positives. For skipped exons on the exon array platform, this field is instead used as a flag to decide whether or not to apply hybridization filters. P = 1 ignores these filters, 0 < P < 1 applies them (recommended).
FC Fold-change cutoff for significance. Default is 1.5.
Limits: x-minx-max, y-maxy-max) Leave these fields blank for the default behavior, which is to use a plotting window that contains all the points. Alternatively, you can specify a different boundary for any of the four sides.
Limit by ID Limit by ID allows you to restrict which points are plotted. Default is plot all points for which there are data, but you can supply a list

of IDs instead that you want to see, and only plot those points. These IDs might be, for example, the first column of a table browser from another comparison. In this way you can examine a gene set of interest within your data. The IDs can be uploaded or pasted (choose from drop-down menu). Pasted IDs can be separated by any whitespace. For uploaded IDs, the first line of the file is checked. If any (tab-separated) field matches /^cluster?id$/i (for example ID or clusterID), then that field is selected from the rest of the lines of the (tab-separated) file. Otherwise the file is parsed as whitespace-separated IDs.

width Width of the image in pixels
height Height of the image in pixels
Names Check the box to add the names of the genes to the plot. Often this doesn't look good, since the names tend to crowd each other out. In that case you can get the name lists by clicking the action buttons.
y=x Check this box to include the diagonal line y=x, and two other lines parallel indicating the Fold-Change cutoffs (recommended).