Unable to use runExprsMerge() to merge 6 FCS files

[zoqaiyum]

Hi @ytdai

I am trying to use the runExprsMerge() function to merge 6 FCS files that have been exported from FlowJo. This is my code below:

cyt.data <- CytoTree::runExprsMerge(fcs.file, comp = FALSE,
                                    transformMethod = "arcsinh", mergeMethod = "fixed", fixedNum = 10000, showDesc = FALSE)

However, I am getting the following error message and I don't know how to fix this. When I did NCOL(fcs.file) I got 1 as the output and NROW(fcs.file) gave me 6. Could you please help?

Error in (function (..., deparse.level = 1) :
number of columns of matrices must match (see arg 6)

Many thanks.

[ytdai]

Sorry for the late reply. You can try runExprsExtract for one single FCS file. If there is still an error, it is recommended to use flowCore::read.FCS(filename = fcs.file) to check the file integrity.

[zoqaiyum]

Hi @ytdai

I used runExprsExtract and was able to successfully read one FCS file. However, when I used runExprsMerge() to read that same FCS file with more files, I got an error saying my FCS file (which I could read using runExprsExtract) is not a valid file.

Is there a discrepancy between the two functions? How do I read more than one FCS file? Can I read them one by one and then somehow merge them?

Many thanks!

[zoqaiyum]

@ytdai

I am still struggling with the question above.