MASS CYTOMETRY F.A.Q’s:
Q: I am having a hard time installing Cytofkit in R after updating, I am getting the following error:
Error: With R version 3.5 or greater install Bioconductor packages using BioCManager
Error: package ‘Cytofkit’ is not available (for R version X)
A: I suspect this error is due to the lack of up keep by the development team for the original version of Cytofkit. With the release of Cytofkit2 (which is very promising) I think they have shifted their workforce to fixing the bugs with the new program. Until Cytofkit2 is usable (the last time I tried it there were still significant road blocks, see my blog post on the subject) we are stuck using R version 3.5.3 (for Mac users) or 3.5.4 (for PC users) for analysis with Cytofkit. If you’re having this error it’s because you have updated R, completely delete this version from your computer, restart, and download the appropriate version.
Q: I am getting the following error when trying to use PhenoGraph:
Error in (function (…, deparse.level = 1) : number of columns of matrices must match (see arg 2)
A: This error is due to an discrepancy between files in the name or number of channels. I would recommend using the R code "premessa" (the code is available on our CyTOF resources page). You will only need the panel editor feature of the program. Rows will be highlighted when there is some discrepancy between samples, you can edit the marker names so they are exactly the same, or delete channels entirely if they aren’t necessary for your downstream analysis.
Q: I’m having a hard time establishing a connection between R/my plugin folder in FlowJo…
A: We had issues too! Here is a transcript of a conversation we had with FlowJo developers which helped me resolve the issue.
Q: How do you export live, singlet events from FlowJo for downstream analysis?
Q: After customizing marker names in Shinyapp the expression of various markers look different…
A: This is a bug in the recent update of Cytofkit:*DON'T CHANGE THE NAMES OF MARKERS IN SHINYAPP*!
When you edit the marker names in the Shinyapp it changes the order of the variables (as it sorts numerically/alphabetically), so you are then visualizing the marker that is now in the first position, rather than the marker you are intending.
Q: How many events should I input into PhenoGraph?