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How to export your 2D gel data from REDFIN: Excel export
Posted by ludesi in How to's in REDFIN
REDFIN basically offers you four ways of exporting your 2D gel image analysis results.
1. Exporting for picking
2. Exporting to a PDF report
3. Exporting to an Excel spreadsheet
4. Exporting the raw data
In this post we will focus on options 3 and 4, which are probably most attractive to you if you are intending to process the data further. This may include creating more elaborate, user-defined graphs, applying custom-made algorithms, or running more specific statistical analyses.
Depending on if you would like to export all spot volumes in the project or only selected spot data, you should choose between the export option on the start page (exporting the raw data), or the Export To Excel option in the results view.
Let’s look at those two in more detail.
Exporting the raw data
On your REDFIN start page you will see several different project specific actions listed on the right side of every analyzed project. One of these actions is “Export” and indicated by a white arrow in a orange circle.
The red box marks the location of the Export button on the REDFIN start page
For any project that you wish to export the analysis results for you simply click this button and choose if you want to export the data with or without images. A compressed .zip file will be saved to your computer.
When extracting the files you will find one spreadsheet named RawSpotData. This file contains all spot data, including position, border, and normalized volume for each spot in each gel.
In addition, there is a file called SpotVolumeMatrix. This contains only the normalized volumes – arranged in a grid versus each protein ID. This file is more suitable for quick plotting and comparing of volumes for each protein.
If you ran a DIGE experiment, these files will also contain the spot volumes of the cy2 internal standards.
Exporting to Excel from within the Results View
In most 2D gel image analysis workflows you will not want to export the entire data set after you are done finding proteins of interest. Instead, you will probably want to export only those protein ID’s that you deemed significant in one way or another.
The export to Excel option in the Results View will allow you to do just that.
After selecting the comparison you are interested in, filter the list until only proteins of interest are left (although you can of course export the entire list without filtering, if you would want that).
Just underneath the first comparison tab you will see how many spot ID’s are left in the list after filtering.
Remember that if you have star rated spots, you need to make sure to also filter on the star property in order to only export the star rated spots.
When you are ready to export the contents of the list simply click on the little Excel icon located in the top right of the screen.
After choosing where you would like to save the generated file, REDFIN will automatically start exporting all the values that are currently present in the list to an Excel spreadsheet.
The spreadsheet is already pre-formatted, and not only contains general information about the experiment, such as experiment name, comparison, groups, and filter settings used, but also statistics and individual spot normalized spot volumes.
Remember, that the main difference between exporting from that REDFIN start page and exporting from the REDFIN results view, is that exporting from the start page provides you with all the spot volumes from all the gel images in the project, whereas exporting from within the results only focuses on the spot volumes of a (probably) filtered list within a selected comparison.
If you are unsure about anything, don’t hesitate to contact us directly at support@ludesi.com.
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