Sample preprocessing in R #17
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Hi, I would like to run all the analysis with R, without data preparation and export from FlowJo. I was wandering if there is a recommended tutorial to do so? Thanks! Maya |
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Replies: 1 comment 1 reply
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Hi Maya, that's certainly doable! We don't have our own tutorials on the the data cleanup etc in R (which is just a reflection of our personal preference to do the cleanup etc in FlowJo), but there are a number of other tutorials out there. On our CyTOF resources page there is a link to a chapter that covers tools which can facilitate this in R: Data-Driven Flow Cytometry Analysis (Sherrie Wang, Ryan R. Brinkman). That should give a nice run down of where to find resources for each relevant step. In particular, flowAI and flowClean will likely be the most help (they should work on both flow and mass cytometry data). If you get stuck then let us know. Tom |
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Hi Tom, thank you for the quick reply! I decided to run the cleanup stage in FlowJo as well Best, |
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Hi Maya, that's certainly doable! We don't have our own tutorials on the the data cleanup etc in R (which is just a reflection of our personal preference to do the cleanup etc in FlowJo), but there are a number of other tutorials out there. On our CyTOF resources page there is a link to a chapter that covers tools which can facilitate this in R: Data-Driven Flow Cytometry Analysis (Sherrie Wang, Ryan R. Brinkman). That should give a nice run down of where to find resources for each relevant step. In particular, flowAI and flowClean will likely be the most help (they should work on both flow and mass cytometry data). If you get stuck then let us know.
Tom