This is a simple question regarding the syntax of using the transformList.

I loaded my data with a meta data file and transformed it.

flowData <- read.flowSet(path = "170113 HTB1-CC503 AOvPI" , phenoData = "metaData4.txt",                       transformation = F)
 tData <- transform(flowData, transformList(colnames(flowData)[1:3],
                                             asinh))

I was curious to know what the [ ] values represent. Is this taking the first 3 files in my flow set and performing the "asinh" transformation on all three of them together. If that is the case, what is the purpose of the "colnames" command?

Thanks!

I also want to add that I don't think my subsetting is working properly, so I fear that I will have a difficult tim looking at replicates within the same experiment.

sampleNames(flowData) <- as.character(pData(flowData)[,"FILENAME"])
 # Error in `[.data.frame`(pData(flowData), , "FILENAME") : 
 # undefined columns selected

My metadata.file is a .txt file with columns labeled as "FILENAME", "SAMPLE", "STRAIN", "CELLDENSITY","BUFFER", and "STAIN".