Subsetting clusters in flowPeaks
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@hefin-rhys-jones-6636
Last seen 7.2 years ago
Hi! I'm using flowPeaks in combination with flowCore and flowViz to identify clusters in flow cytometry data. I can get adequate clustering of my flow frame, and now I want to get summary statistics for each identified cluster (median fluorescence intensity for each parameter etc.). I can't find any way of subsetting my flow frame to only include particular clusters to get this summary information. Am I able to do this? Any help would be much appreciated. Thank you Hefin Sent from my BlackBerry? smartphone www.blackberry.com
flowCore flowViz flowPeaks flowCore flowViz flowPeaks • 816 views
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@hefin-rhys-jones-6636
Last seen 7.2 years ago
Oh I worked it out, after using the assign.flowPeaks function, I just used: summary(data [assigned == 1]) Thanks Hefin Sent from my BlackBerry? smartphone www.blackberry.com -----Original Message----- From: <h.r.jones@qmul.ac.uk> Sender: <bioconductor-bounces at="" r-project.org=""> Date: Mon, 14 Jul 2014 15:42:22 To: bioconductor at r-project.org<bioconductor at="" r-project.org=""> Reply-To: <h.r.jones at="" qmul.ac.uk=""> Subject: [BioC] Subsetting clusters in flowPeaks Hi! I'm using flowPeaks in combination with flowCore and flowViz to identify clusters in flow cytometry data. I can get adequate clustering of my flow frame, and now I want to get summary statistics for each identified cluster (median fluorescence intensity for each parameter etc.). I can't find any way of subsetting my flow frame to only include particular clusters to get this summary information. Am I able to do this? Any help would be much appreciated. Thank you Hefin Sent from my BlackBerry? smartphone www.blackberry.com _______________________________________________ Bioconductor mailing list Bioconductor at r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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shadhiksk • 0
@shadhiksk-13179
Last seen 4.3 years ago

Hi Hefin,

I am facing a problem of using flowpeaks for a flowframe to get the required clusters. 

like here 

fp2<-flowPeaks(barcode[,c(1,3)]) how can I replace barcode with a flowframe? can I know the format for R code?

and fpc<-assign.flowPeaks(fp2,fp2$x)  what is fp2$x here mean?

May I know

fp.z<-flowPeaks(asinh(samp@exprs[,3:4]))  let us say the 2nd column is SSC-A and 4th is FITC-A how can I plot between FITC-A ans SSC-A?

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