I appreciate your help. I'm still pretty new to R programming so I will do my best to follow the posting guide.
I was able to troubleshoot my previous error with your help, but now I have some problems with evalCluster(). I tried my best to fix the following issue:
Error in evalCluster("example.FCS3.fcs",fp2$peaks.cluster,method="Vmeasure", fp2$peaks.cluster, method = "Vmeasure") : the length of gs should be the same as cand
after checking ?evalCluster() I realized that somehow the length for example.FCS3.fcs or fcsorig (gs) is not the same as fp2$peaks.cluster (cand).. I'm not exactly sure what's going on. Is there anything I can do to fix this?
I tried to cutdown my gs by trying
fcsorig <- fcs@exprs[,7:11] # fcs is my read.FCS file from imported FCS3 file from flowJo
but it didn't work. Any suggestions?