Creating a flowSet
Entering edit mode
mbxtp1 • 0
Last seen 7.6 years ago

I have tried using the read.flowSet() command to read in multiple .fcs files but I keep getting the following error:

all <- read.flowSet(files=NULL,path=".",pattern=".fcs")
Error in asMethod(object) :
  The individual flowFrames do not contain identical stains.
In addition: Warning message:
In ucol == sort(colNames[, 1]) :
  longer object length is not a multiple of shorter object length

The files all follow the same format, only differences being the data and number of cells. They have the same row and column names despite the error message.

> unstained1
flowFrame object 'Unstained.fcs'
with 16462 cells and 14 observables:
            name desc     range minRange  maxRange
$P1         Time <NA> 536870912        0 536870911
$P2          FSC <NA> 536870912        0 536870911
$P3          FSC <NA> 536870912        0 536870911
$P4          SSC <NA> 536870912        0 536870911
$P5          SSC <NA> 536870912        0 536870911
$P6   FL1-Height <NA> 536870912        0 536870911
$P7   FL2-Height <NA> 536870912        0 536870911
$P8   FL4-Height <NA> 536870912        0 536870911
$P9   FL6-Height <NA> 536870912        0 536870911
$P10  FL7-Height <NA> 536870912        0 536870911
$P11 FL10-Height <NA> 536870912        0 536870911
$P12 FL11-Height <NA> 536870912        0 536870911
$P13 FL12-Height <NA> 536870912        0 536870911
$P14 FL14-Height <NA> 536870912        0 536870911
101 keywords are stored in the 'description' slot

On the contrary, I am able to read in the files individually using the command below:

unstained1 <- read.FCS("Unstained.fcs",transformation="linearize")

I would like to perform probability binning but it requires a flowSet to be created, yet I cannot surpass this step. Any suggestions would be a great help! Thanks in advance.

flowcore flow cytometry flowstats read.flowset() • 1.6k views

Login before adding your answer.

Traffic: 473 users visited in the last hour
Help About
Access RSS

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

Powered by the version 2.3.6