Entering edit mode
I'm using flowClust to identify cell subsets in flow data. I use the untreated samples to obtain a prior, which works well. However, when running flowClust on the remaining samples with the prior, I get this message:
"randomStart>0 has no effect when using a prior. Labels are initialized from the prior.
Using the parallel (multicore) version of flowClust with 4 cores"
I've tried setting different values for randomStart but it didn't help.
It's not a problem per se.. everything still works fine and the clustering looks good but it just clutters up the console (ocd, I know!).
Thoughts?
Hmm, I tried that but I still get the warning. This was my flowClust call:
prior<-flowClust2Prior(flowClust(all_data[[which(phenoData(all_data)$promoter=='none')]],
varNames=c('FSC-A','SSC-A'),
K=numclusters,
nu=Inf,
level=outlierlev,
min=minvals,
max=maxvals),
kappa=1);
res_all<-fsApply(all_data,function(x)flowClust(x,varNames=c('FSC-A','SSC-A'),
K=numclusters,
level=outlierlev,
min=minvals,
max=maxvals,
randomStart=FALSE,
prior=prior,
usePrior='yes'));
Thanks,
Turns out there was a bug in the code throwing the warning unnecessarily. I've pushed a fix, and it should appear some time tomorrow. Now setting randomStart=FALSE or 0 should suppress the warning properly.
Greg