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 <wjia...@fhcrc.org> > To: <bioc-devel@r-project.org>, <niklaus.hurlim...@chuv.ch> > Subject: Re: [Bioc-devel] Fwd: read fcs file from CyTOF with > Message-ID: <54136b19.3030...@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.hurlim...@chuv.ch > >> <mailto:niklaus.hurlim...@chuv.ch>> > >> *Subject: **[Bioc-devel] read fcs file from CyTOF with* > >> *Date: *September 12, 2014 at 6:28:49 AM PDT > >> *To: *"bioc-devel@r-project.org <mailto:bioc-devel@r-project.org>" > >> <bioc-devel@r-project.org <mailto:bioc-devel@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 [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
