I would like to learn how to use flowCore etc to analyze my flow cytometry data and I am currently using the "flowCore: data structures package for flow cytometry data" (20/5/14) [the 24/10/14 version seems more or less similar].
I used the read.flowSet() function as reported at page 11, but I got exactly the results from the vignette rather than from actual files, which means I am not reading from the working directory. I reckon I should use the 'files', 'name.keyword' and 'phenoData' arguments but I don't know how.
So far, what I have tried is:
fs <- read.flowSet(
path = system.file("extdata", "compdata", "data", package="flowCore"),
name.keyword = "SAMPLE ID",
phenoData = list(names = "SAMPLE ID", Filenames = "$FIL")
name names Filenames NA NA NA 060909.001 fitc fitc fitc 060909.002 pe pe pe 060909.003 apc apc apc 060909.004 7AAD 7AAD 7AAD 060909.005
fcs.loc <- system.file("extdata",package="flowCore") file.location <- paste(fcs.loc, dir(fcs.loc), sep="/") samp <- read.flowSet(file.location[1:3]) pData(phenoData(samp))
Whose result is:
name 0877408774.B08 0877408774.B08 0877408774.E07 0877408774.E07 0877408774.F06 0877408774.F06
The name of the files I am using, present in the working directory, are:
sample.set <-c( "Compensation Controls_HOE 405-450,2f,50 Stained Control_004.fcs", "Compensation Controls_PY 488-575,2f,26 Stained Control_005.fcs", "Compensation Controls_Unstained Control_003.fcs", "samples_stimulated_001.fcs", "Specimen_001_stim_002.fcs", "Specimen_001_unstim_001.fcs" )