All, flowFrames can be created by .FCS files using read.FCS, I was wondering if I could create a flowFrame from a matrix, The matrix will be in the identical form of the exprs() output for a flowFrame, so that I could extract data to a raw matrix, custom-manipulate, then remake the flowFrame and use flowCore functions again. I am sure I am overlooking some simple function here, any help? Best reguards, Mark Allenby PhD, Imperial College London

Hi Mark, I'm not sure if you've seen the flowCore reference guide [1] but it explains how to create a flowFrame. In addition to your matrix of observations, you also need to fill the slots for 'parameters' and 'description'; this can done using either the 'new()' command or a built-in flowFrame constructor. [1] http://www.bioconductor.org/packages/release/bioc/manuals/flowCore/man /flowCore.pdf, see pg 51 On Tue 08 Jul 2014 01:44:57 PM EDT, Allenby, Mark wrote: > All, > > flowFrames can be created by .FCS files using read.FCS, I was wondering if I could create a flowFrame from a matrix, The matrix will be in the identical form of the exprs() output for a flowFrame, so that I could extract data to a raw matrix, custom-manipulate, then remake the flowFrame and use flowCore functions again. > > I am sure I am overlooking some simple function here, any help? > > Best reguards, > > Mark Allenby > PhD, Imperial College London > > _______________________________________________ > 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

|openCyto| package has an internal function for loading matrix(first row must contains the channel or marker name) from csv. e.g. |> fr <- openCyto:::.read.FCS.csv("local_output/test.csv") > fr flowFrame object'anonymous' with2 cells and2 observables: name desc range minRange maxRange FSC-A FSC-ANA 11 1 11 SSC-A SSC-ANA 12 2 12 1 keywords are storedin the'description' slot | On 07/09/2014 03:00 AM, bioconductor-request@r-project.org wrote: > Subject: > [BioC] How to write a flowFrame from a matrix > From: > "Allenby, Mark" <mark.allenby@imperial.ac.uk> > Date: > 07/08/2014 10:44 AM > > To: > "bioconductor@r-project.org" <bioconductor@r-project.org> > > > All, > > flowFrames can be created by .FCS files using read.FCS, I was wondering if I could create a flowFrame from a matrix, The matrix will be in the identical form of the exprs() output for a flowFrame, so that I could extract data to a raw matrix, custom-manipulate, then remake the flowFrame and use flowCore functions again. > > I am sure I am overlooking some simple function here, any help? > > Best reguards, > > Mark Allenby > PhD, Imperial College London > > [[alternative HTML version deleted]]