[Bioc-devel] read fcs file from CyTOF with

Josef Spidlen jspidlen at bccrc.ca
Tue Sep 16 11:27:35 CEST 2014

Hi Niklaus,
we are routinely using read.FCS() to read FCS data from a CyTOF. I'd
suggest checking that you are using the latest version of flowCore. Also,
you may want to inspect the files in some other text/hex editor. The first
3 bytes of the file should read "FCS" (followed by version of the standard).


Josef Spidlen, Ph.D.
Staff Scientist, Terry Fox Laboratory, BC Cancer Agency
675 West 10th Avenue, Vancouver, BC, V5Z1L3, Canada
Tel. +1 604-675-8000, ex. 7755

Date: Fri, 12 Sep 2014 14:52:25 -0700
> From: Mike <wjiang2 at fhcrc.org>
> To: <bioc-devel at r-project.org>, <Niklaus.Hurlimann at chuv.ch>
> Subject: Re: [Bioc-devel] Fwd:  read fcs file from CyTOF with
> Message-ID: <54136B19.3030707 at fhcrc.org>
> Content-Type: text/plain; charset="UTF-8"
> 'flowCore' does support CyTOF fcs as long as it follows the fcs
> standard.( "FCS2.0", "FCS3.0" and "FCS3.1")
> Based on your check by 'isFCSfile',  Your fcs file is probably not any
> one of these.
> >> *From: *Hurlimann Niklaus <Niklaus.Hurlimann at chuv.ch
> >> <mailto:Niklaus.Hurlimann at chuv.ch>>
> >> *Subject: **[Bioc-devel] read fcs file from CyTOF with*
> >> *Date: *September 12, 2014 at 6:28:49 AM PDT
> >> *To: *"bioc-devel at r-project.org <mailto:bioc-devel at r-project.org>"
> >> <bioc-devel at r-project.org <mailto:bioc-devel at r-project.org>>
> >>
> >> I tried to upload an fcs-file generated by CyTOF with read.FCS() from
> >> the flowCore package. If I do the check with isFCSfile(files) it
> >> gives me the answer FALSE, obviously it does not recognize the fcs
> >> file as such. I am quite new in handling such type of data.
> >> My question is the flowCore package compatible with CyTOF fcs or not?
> >>
> >> Your comments are very much appreciated
> >>
> >> Niklaus Hurlimann

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