Error in (function ...

[LogIN-]

Hello, When using cytofkit via cytofkit_GUI and after selection all FCS files and markers, when analysts starts I get following error:

> library("cytofkit")
Loading required package: ggplot2
Loading required package: plyr
> cytofkit_GUI()
Input arguments:  
* Project Name: cytofkit_high 
* Input FCS files for analysis:
   -xyz.fcs
   -xyz.fcs
   -xyz.fcs
   -xyz.fcs
   -xyz.fcs
   -xyz.fcs
   -xyz.fcs
   -xyz.fcs
   -xyz.fcs
   -xyz.fcs
   -xyz.fcs
   -xyz.fcs
   -xyz.fcs
   -xyz.fcs
   -xyz.fcs
* Markers:
   -(xy)Dd<xy>
   -(xy)Dd<xy>
   -(xy)Dd<xy>
   -(xy)Dd<xy>
   -(xy)Dd<xy>
   -(xy)Dd<xy>
   -(xy)Dd<xy>
   -(xy)Dd<xy>
   -(xy)Dd<xy>
   -(xy)Dd<xy>
   -(xy)Dd<xy>
   -(xy)Dd<xy>
   -(xy)Dd<xy>
   -(xy)Dd<xy>
   -(xy)Dd<xy>
   -(xy)Dd<xy>
   -(xy)Dd<xy>
   -(xy)Dd<xy>
   -(xy)Dd<xy>
* Data merging method: ceil 
* Data transformation method: cytofAsinh 
* Dimensionality reduction method: tsne 
* Data clustering method(s): Rphenograph ClusterX DensVM 
* Data visualization method(s): pca isomap tsne 
* Subset progression analysis method: NULL 

Extract expression data...
Error in (function (..., deparse.level = 1)  : 
  number of columns of matrices must match (see arg 4)

Why is this happening?

[MattMyint]

Hi, sorry for the delay in response

Its possible that your fcs files have some markers that are not common to all, which prevents cytofkit from merging the expression data from all of them together.

You can consider making copies of the fcs files which exclude these non-overlapping markers and running these through cytofkit.

Regards, Matthew

[MattMyint]

Closing the issue, but if the problem persists feel free to reopen