Jump to content
Beckman Coulter User Forums

Percentages within gates


Recommended Posts

Anyone know of a way to exclude certain events from gate percentage calculations? For example, if I gate around debris, then plot out NOT DEBRIS on a 45 vs SSC, then gate around lymphocytes on the 45 vs SSC, then gate on CD19 positive lymphocytes, can I get the CD19 cells as a percentage of NOT DEBRIS without having to manually calculate myself based on the total numbers of CD19 and NOT DEBRIS?

Link to comment
Share on other sites

I think based on what you're describing that is what you're getting. Use a gate statistics plot and turn on the full logic option. You should be able to see the full expanded logic for the population you're looking at, which you should be able to use to confirm that you're excluding the debris.

Link to comment
Share on other sites

  • 3 weeks later...

Say I set up three dot plots (A, B, and C). A is [ungated] SSC vs CD45. In plot A I create a gate labeled Viable. Plot B is [Viable] SSC vs CD45. In plot B I create a gate labeled Lymphocytes. Plot C is [Lymphocytes] CD19 vs kappa. In plot C I create a gate labeled CD19+Lymphocytes. When attempting to determine statistics for CD19+Lymphocytes, I can only figure out how to determine the Number, the % Total, and the % Gated based on [Lymphocytes]. How do I determine the % Gated based on [Viable]? Obviously when I do a % Gated based on [Lymphocytes] the [Viable] gate is factored in, but I want a percentage of all the cells in [Viable], not just a percentage based on the [Lymphocytes] within [Viable].

Link to comment
Share on other sites

I understand better now. You want, in this case, a "percent grandparent". This is a feature we're considering, but isn't currently available. However, you can get this statistic (and many other related ones) using the Information Table. Add an Information Table to your sheet. Click on the left side of the highlighted first row, it should let you type. Enter a name, whatever you want, I used "CD19+Lymphocytes % Viable". Now click on the right side of that line (or just press the Tab key when the left side is highlighted) and enter this text (easiest to copy/paste): "=COUNT("CD19+Lymphocytes", 1)/COUNT("Viable", 1)*100" (You shouldn't use the outer quotes.) That should give you the start of a table giving you the key statistics you want. If you just want simple statistics (such as the % gated for Lymphocytes) you can just use the "<Add Statistic>" link in the lower left of the Information Plot. Overall this is a little less convenient than clicking a "% grandparent" checkbox would be, but you get a lot more power.

 

A few tips:

1) You can press F1 when the table is highlighted to get help on the available functions, but sometimes it's just easiest to add a statistic for one of the terms you want, and then copy/paste the text out of the line that's created for you.

2) It can be difficult to work within the confined space of the Information Table. For more complicated expressions it's easier to use CTRL-A/CTRL-C/CTRL-V and a notepad session to build and establish your expressions.

3) Some people use this feature to calculate much more complicated "Lymphosums" where they identify sub-populations of the lymphs and then report out percentages of those sub-populations relative to the total of all of them - ignoring unclassified cells that might be included in a normal SS/CD45 Lymph gate.

 

If you have multiple files that you want to do the same thing with, and you're unfamiliar with the Information Plot, it might be useful to experiment with it when you export statistics from a group of files. Normally your statistics under a plot go into a Statistics.csv file, but the contents of the Information Plot go into an Information.csv. That table is pivoted relative to what you see on the plot sheet. Each row label becomes a column header, and each row value pivots to go under the appropriate header. Each file gets one line in the resulting table. It's a very powerful way to get only the statistics you want in a convenient table form for all the files in your analysis. The Information Plot works similarly in the batch processing activity as well.

 

Regards,

Ernie

Link to comment
Share on other sites

Archived

This topic is now archived and is closed to further replies.

×
×
  • Create New...