Question: Load FlowCore to read .fcs files in R
0
gravatar for Bayram Sarilmaz
15 months ago by
turkey
Bayram Sarilmaz0 wrote:

I'm trying to load flowCore library to read a flow cytometry file (.fcs), but I'm getting the following error:

> library (flowCore)
Error: package or namespace load failed for ‘flowCore’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called ‘mvtnorm’
In addition: Warning message:
package ‘flowCore’ was built under R version 3.4.3 

> fcs1 <- read.FCS("MyFACsFile.fcs",transformation=FALSE)
Error in read.FCS("MyFACsFile.fcs", transformation = FALSE) : 
could not find function "read.FCS"

I tried re-installing the package, but still it didn't work, although I was able to read the same file using the same code few months ago. Any suggestions on what the problem is? and how to read .fcs files in R?

flowcore R flow cytometry • 1.4k views
ADD COMMENTlink modified 15 months ago • written 15 months ago by Bayram Sarilmaz0

Hi,

Something went wrong during the installation of flowCore. You need to solve all the dependencies that flowCore will complain about. For example, you should install the mvtnorm package, either using install.packages("mvtnorm") or BiocInstaller::biocLite("mvtnorm"). Then try again library(flowCore), and solve any remaining dependency.

The read.FCS is unknown because flowCore was not loaded.

ADD REPLYlink written 15 months ago by SamGG190

Thanks. I installed the dependency, and was able to load flowCore. However, I'm still unable to read the file. Getting the following error: Error in read.FCS("MyFACsFile.fcs", transformation = FALSE) :  'MyFACsFile.fcs' is not a valid file. Although I was able to access the exact same file before!

ADD REPLYlink written 15 months ago by Bayram Sarilmaz0
1

Try the absolute full path to your fcs file.

ADD REPLYlink written 15 months ago by Jiang, Mike1.2k
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