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Before I go onto making gates, which is kind of the funnest part of FlowJo, in my opinion. You're exploring your data, looking at the distributions that you've stained for. I want to mention just one or two things about keyword information.

I have a tendency to create many keywords when I acquire the data, so that all of the data files are labeled with pertinent information like patient ID and time point, and draw date of the specimen. If you do that on the front end, you can display any of that metadata information by going to the Configure tab, Edit Columns feature. When I open Edit Columns, it gives me a list on the left of all of the potential headers in that FSC file. Dialer signs are things that are required by the FCS standard. The reagent labels can be found with the parameter names plus the reagent tag here, so if I double click in order to visualize what is labeled there for the PacBlue reagent for example, I can double click on that column. It'll move it over to the right to columns to display, and then I can press okay. It'll show me the reagent label for that channel. In this case, PacBlue represents the CD8 distribution.

Now I also can add additional keywords with more information like patient ID. I'm going to go to Edit Columns again, and I'm going to scroll all the way down past the dollar signs into a group of keywords that I've made for the samples that start with asterisks. I use asterisk at the beginning just to group them in the list so I can access them easier, and things like patient ID are really important. Maybe the STM conditions that we talked about for this assay. I'll go down, this was a plate based assay so we'll look at the well IDs as well. We've got PID, STM, and well ID here. When I press okay, then I get this keyword lists, and which shows me the patient IDs and the STM conditions and the wells.

If you need to change any of this information, you can always just type in information here and change it. If I mislabeled something I can display my reagent label and I can change it here for each of those samples. If you did not add any keyword and you want to do them after the fact, I can go to my workspace tab where there is a keyword band of functions. One of those is add a new keyword, so just the plus key, add keyword. It'll give me a naming field where I'm just going to type in “my new keyword”, and press okay. Then you get this column with that header, whatever you name that keyword, and you can type in information, one, two, three, four. You can get a drop down list of those values once you've typed them.

You can also apply a single value to the entire group of samples by typing it in, highlighting it, and then going to that keywords band, and then copying that value to the group, so applying that down. Now I have the value of one applied all the way through, which is exactly if I wanted to change that reagent column, you can go to CD45. If that was mislabeled and I wanted to apply it, then you just copy that value to the group after highlighting it. Same deal if I want to go back, CD8. Type it once, highlight it, and then copy the value to the group.

Now the important thing here is that I can use these keywords to say, sort my list. If I right click on the header, I can sort by the keyword information. Then I can also use these keywords in a batching function to report in a specialized way. Even in my tables. What if I want to put this information into the report that I generate with all of the analyzed numbers out of my analysis. Then I can do that in the table editor.

Just know that you can attach all these tributes using the keywords band to your FCS files, and they will help you organizing your data set in a more robust fashion.