Error when using read.FCS
1
0
Entering edit mode
Pepijn • 0
@85919942
Last seen 3.8 years ago

Hello everyone,

I'm trying to read my FCS file of spleen data into R, but I'm getting this error. I exported the FCS file with the compensated parameters from Flowjo. If I export the uncompensated data from Flowjo, it reads the FCS without any errors. I'm a student that is quite new to this, so I sadly can't provide you with alot of details. I wondered if anyone knew how I could fix this error.

myfile <- "D:/BPS/RP1/Autogating/Databank/test2.fcs"
fcsfile <- read.FCS(myfile)

Error in string_to_spill(txt) : 
  bad lexical cast: source type value could not be interpreted as target
In addition: There were 50 or more warnings (use warnings() to see the first 50)
compensation flowCore FlowCore read.FCS • 1.7k views
ADD COMMENT
1
Entering edit mode
SamGG ▴ 350
@samgg-6428
Last seen 6 days ago
France/Marseille/Inserm

Hi,

You should select a FCS 3.0 as file format and export all uncompensated channels. The compensation matrix is saved within the FCS, so that you could easily compensate the data when reading the FCS file in R.

More on that in paragraph 5 of the flowCore vignette.

The current error states that the compensation/spillover matrix has an unattended shape for read.FCS function.

Best.

ADD COMMENT

Login before adding your answer.

Traffic: 810 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6