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Question: Creating a flowSet
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gravatar for mbxtp1
2.6 years ago by
mbxtp10
mbxtp10 wrote:

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.

ADD COMMENTlink written 2.6 years ago by mbxtp10
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