Update:
So after you mentioned checking the version of FLowCore. I simply updated FlowCore with
- Code:
install.packages("devtools")
devtools::install_github("RGLab/flowCore", ref = "trunk")
and reloaded the required packages and bingo it worked. FCS files are exporting correctly now. Thank you
The problem pervious to this was that not only was all the data corrupt for each parameter, but also the FCS files were missing the new parameters such as Phenographcluster_ID and TSNE1 etc. Interestingly I often used strange characters. Since the issue is fixed I suppose there is no need to test if it was just to weird character use.
Thanks for the reply, I also have another bug that I want to get advice on. It regards renaming Markers.
When I rename the marker names in the shiny App the markers get renamed but now become jumbled up. For example, if I rename Y89<CD45> to CD45, and so on, this works as there is now a list of simple names, including "CD45". However, when looking at the expression plots I see that the marker called CD45 is obviously not CD45 but has been mixed up with another marker. This happens for every marker, thus making the analysis unusable. Perhaps there is another way to rename the channels outside of R, but it would be great if this bug could be reported as it could catch out a lot of people and lead to erroneous conclusions.
I could use the great little permessa panel but while I can simplify the parameter name from e.g. "Di209<CD11c>" to "CD11c<CD11c>" in permessa it still appears as "CD11c<CD11c>" in cytofkit rather than the publication-ready "CD11c".