Error in gating section of flowcore package

[synatkeamsk]

Dear Authors,

I am replicating your code in FlowCore "https://www.bioconductor.org/packages/release/bioc/vignettes/flowCore/inst/doc/HowTo-flowCore.pdf. I have run from first section until section 8, when I started to get error. Im not sure how to fix it. Hope you could help.

Kind Regards,

Synat,

[DillonHammill]

Looks like your comp object is for data in the previous section of the vignette. You will need to update it after loading in the new data so that the column names match the channels in the new flowSet.

comp <- spillover(fs[[1]])
comp <- comp[!sapply(comp, "is.null")][[1]]
gs <- compensate(gs, comp)

[synatkeamsk]

Thanks 🙏, you. I'll try again tomorrow and let you know the outcome.

Kind Regards,

Synat

[synatkeamsk]

Sorry, I am still getting error when I run chnls <- parameters(comp). The code from the vignette.

library(flowWorkspace)
fcsfiles <- list.files(pattern = "CytoTrol",
system.file("extdata",
package = "flowWorkspaceData"),
full = TRUE)
fs <- read.flowSet(fcsfiles)

gs <- GatingSet(fs)
gs

I run new code based on your suggestions.

comp <- spillover(fs[[1]])
comp <- comp[!sapply(comp, "is.null")][[1]]
gs <- compensate(gs, comp)
fs_comp <- getData(gs)

8.3 transform the data

biexpTrans <- flowJo_biexp_trans(channelRange=4096, maxValue=262144
, pos=4.5,neg=0, widthBasis=-10)
chnls <- parameters(comp)  # error here ! 

Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘parameters’ for signature ‘"matrix"’

I am a beginner R person, so it is hard to understand what is going on here. Sorry and thank for your help.

Kind Regards,

synat

[DillonHammill]

comp is a matrix so the channel names can be accessed as follows:

chnls <- colnames(comp)

[synatkeamsk]

Thank you. it worked now. appreciated your kind assistance.