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posted by Jennifer Davis
on April 21, 2010 11:43:59
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coming soon- Histogram overlays are another way of assessing the signaling response of a particular protein in each of the conditions measured. In this case, we are interested in comparing one parameter at a time. Histogram overlays on Cytobank color peaks based on a quantitative comparison between the populations shown in the rows of the overlay. The statistic used for the comparison can be customized and the data table exported, as with heatmaps.
- Let's start with the saved illustration from the previous section. In the experiment summary page, click on Edit next to "contour plots".
- Change the plot type to Histogram overlay and click on Update Illustration.
- Set the X axis to Use Panel/Channel Values.
- Move the boxes in the "Figure Dimensions" area until "Populations" is labeled "Columns", "Dosages" is labeled "Overlaid", "Channels" is labeled "Table 1", and "Individuals" is labeled "Table 2". Click "Update Illustration".
- Select CD4+ cells and CD8+ cells in Populations.
- We'd like to swap the order of CD4 and CD8. Still in "Layout Placeholders", drag the "CD4+ cells" label and put it on top of the "CD8+ cells" label. They'll swap places.
- Make sure all dosage tags are selected in Dosages.
- Select Donor 1 from Individuals.
- The illustration tab will display a histogram overlay for each of the proteins selected in the channels dimension. Each overlay will contain the
conditionsdosages selected in theconditionsdosages dimension. The table underneath the histogram overlay is reporting a statistic. In this case each value in the table is the median intensity of the corresponding phosphoprotein andcondition.dosage. A more useful statistic would be how much more a protein responded when compared to its unstimulated state (fold change). Configure this by choosing Fold change equation in the "Plot Statistics" section on the left menu bar and choosing the First Row as the control. Click on Update Illustration to see the results. - Save the illustration as "histogram overlays".
