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How do you calculate the fold-change?
Posted by ludesi in How to's in REDFIN
The fold-change value you see in REDFIN, is calculated from the mean normalized volumes between the groups of a particular comparison.
In the case where there are more than two groups, the maximum of these changes is shown. For example, if you have 3 groups and the average volume for a particular spot within one group is 100, 300, and 200, respectively, then the fold change will be 300/100, which is 3.
You are of course able to calculate individual fold changes by exporting the data to an Excel spread sheet.
REDFIN doesn’t present you with negative or positive fold-changes, because the fold-change is always relative depending on your frame of reference. Instead you are able to search for proteins that are being specifically up- or down-regulated using the Expression Profile Filter.
Searching for proteins with a specific fold-change and relative expression
1. Set your fold-change filter by choosing a number from the drop down or typing one in the box and hitting ENTER. In the following example, we set the fold-change as 2.
Working in the list view in REDFIN
The list now only shows protein spots with a fold-change of 2 or more. Note that the expression symbol shows that the direction of the change between Group 1 (green dot) and Group 2 (purple dot) can be both positive and negative.
2. Click on the “Push to set profile filter button” and set the filter to show only spots that are up-regulated in Group 2 vs. Group 1. Click OK.
The Expression Profile Filter tool in REDFIN
3. Now the list only shows protein spots that have a fold change of 2 or more and that are up-regulated in Group 2 relative to Group 1.
List view in REDFIN after setting a protein expression and fold-change filter
For more information on how to work with the Protein Expression Filter in REDFIN check out the blog post “Exploring Protein Expression Profiles“.
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