Question: flowCore - how to see the marker names?
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gravatar for Anne
11.5 years ago by
Anne60
Anne60 wrote:
Hi, I am having problems in finding the marker names in a flowFrame. (The marker names mapped onto the channel names - i.e.FL1-H, FL2-H, FL3-H and FL4-H). I wrote the code: FCS <- read.FCS(subfilesdir2) FCS featureNames(FCS) and got this output - but it does not seem to show any new names (i.e CD45), so am I doing the right thing: flowFrame object 'P:/Projekter/Scientific Projects/AML_subgroup specific gene expression_2008/Part A/Data/Raa data/AML_FC_Herlev/de39patienter/BH13100/BH13100.002' with 100000 cells and 7 observables: name desc range minRange maxRange $P1 FSC-H FSC-Height 1024 0 1023 $P2 SSC-H SSC-Height 1024 0 1023 $P3 FL1-H FL1-Height 1024 1 10000 $P4 FL2-H FL2-Height 1024 1 10000 $P5 FL3-H FL3-Height 1024 1 10000 $P6 FL1-A <na> 1024 0 1023 $P7 FL4-H FL4-Height 1024 1 10000 132 keywords are stored in the 'descripton' slot > featureNames(FCS) $P1N $P2N $P3N $P4N $P5N $P6N $P7N "FSC-H" "SSC-H" "FL1-H" "FL2-H" "FL3-H" "FL1-A" "FL4-H" Thanks in advance /Anne [[alternative HTML version deleted]]
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ADD COMMENTlink modified 11.5 years ago by Nolwenn LeMeur140 • written 11.5 years ago by Anne60
Answer: flowCore - how to see the marker names?
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gravatar for Nolwenn LeMeur
11.5 years ago by
Nolwenn LeMeur140 wrote:
Hi Anne, The parameter annotation of a flowframe is stored in an annotated dataframe. You can access the information using the pData function: pData(parameters(FCS)) see the flowFrame-class man page for more details Nolwenn Anne wrote: >Hi, > >I am having problems in finding the marker names in a flowFrame. >(The marker names mapped onto the channel names - i.e.FL1-H, FL2-H, FL3-H >and FL4-H). > >I wrote the code: > >FCS <- read.FCS(subfilesdir2) >FCS >featureNames(FCS) > >and got this output - but it does not seem to show any new names (i.e CD45), >so am I doing the right thing: > >flowFrame object 'P:/Projekter/Scientific Projects/AML_subgroup specific >gene expression_2008/Part A/Data/Raa >data/AML_FC_Herlev/de39patienter/BH13100/BH13100.002' >with 100000 cells and 7 observables: > name desc range minRange maxRange >$P1 FSC-H FSC-Height 1024 0 1023 >$P2 SSC-H SSC-Height 1024 0 1023 >$P3 FL1-H FL1-Height 1024 1 10000 >$P4 FL2-H FL2-Height 1024 1 10000 >$P5 FL3-H FL3-Height 1024 1 10000 >$P6 FL1-A <na> 1024 0 1023 >$P7 FL4-H FL4-Height 1024 1 10000 >132 keywords are stored in the 'descripton' slot > > >>featureNames(FCS) >> >> > $P1N $P2N $P3N $P4N $P5N $P6N $P7N >"FSC-H" "SSC-H" "FL1-H" "FL2-H" "FL3-H" "FL1-A" "FL4-H" > >Thanks in advance > >/Anne > > > [[alternative HTML version deleted]] > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > >
ADD COMMENTlink written 11.5 years ago by Nolwenn LeMeur140
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