[Bioc-devel] read fcs file from CyTOF with

[Josef Spidlen]

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).

Cheers,
Josef

--
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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