Question: flowFit channel name needs to match keyword value in order for parentFitting to work?
1
gravatar for erickttr
4.3 years ago by
erickttr0
United States
erickttr0 wrote:

It seems as though it is necessary for a column name (e.g., a channel) to match exactly the desc keyword in order for the function to work.  I think a workaround would be to change the "desc" keyword in $P3 for all the flowFrame objects from "CFSE-FITC" to "FL1.H"  But I do not know how to edit the files.  I could do that on the original flowJo software, but I don't have it -- the FSC file was created on the computer in the core facility and I don't have access to it anymore.  I tried to use my Terminal/unix commands to gsub(/CFSE-FITC/,"FL1.H") ... but that changed the file kind from Flow Cytometry standard data to a Unix executable file .... and then it was not readable by flowCore package. The only way to change it back to the appropriate file kind was to revert it (which removed the gsub command).  Any help -- either with flowFit  OR on how to change the desc from "CFSE-FIT" to "FL1H" .... would be much appreciated!

> cd14[[14]]
flowFrame object 'Data.014'
with 10691 cells and 5 observables:
     name       desc range  minRange maxRange
$P1 FSC.H FSC-Height  1024 0.5945472      4.5
$P2 SSC.H SSC-Height  1024 0.5945472      4.5
$P3 FL1.H  CFSE-FITC  1024 0.5276393      4.5
$P4 FL2.H    TNFa PE  1024 0.5276393      4.5
$P7 FL4.H   CD14 APC  1024 0.5276393      4.5
119 keywords are stored in the 'description' slot

> summary(cd14[[14]])
        FSC.H SSC.H  FL1.H  FL2.H  FL4.H
Min.    3.241 2.778 0.5276 0.5276 0.6794
1st Qu. 3.368 3.278 1.9420 0.7883 1.8800
Median  3.483 3.437 2.1900 1.0540 2.0960
Mean    3.523 3.468 2.1700 1.0500 2.1220
3rd Qu. 3.647 3.631 2.4620 1.3030 2.3350
Max.    4.076 4.202 3.2340 3.2650 3.7030

> parent.fitting.cfse<- parentFitting(Data(wf[["CD14+"]])$Data.014, channel="FL1.H")
parentFitting: No dataRange provided. Setting range from channel range: 4.5
Error in .getKeywordValue(flowframe, channel, "M") : 
  Channel FL1.H is not present in flowFrame keywords!

> parent.fitting.cfse<- parentFitting(Data(wf[["CD14+"]])$Data.014, channel="CFSE-FITC")
Error in .local(.Object, ...) : 
  Invalid channel name not matching the flowFrame:
    CFSE-FITC
ADD COMMENTlink written 4.3 years ago by erickttr0
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