[BioC] problems reading fcs files / flowcore / read.fcs (David Corne)

[Josef Spidlen]

Hi David,
is the problem related to empty keyword values as reported by Kieran on 
06/13/2012 12:41 PM (i.e., do you see an error like "Error in 
fcs_text_parse(txt) : ERROR! no end found")?

Mike (Jiang), are you considering "fixing" it (e.g., as I suggested on 
Mon, 18 Jun 2012 15:00:57)?
I mean, I know it's not your fault that these instrument vendors are 
breaking the standard by allowing empty keyword values. However, at the 
end, it will be flowCore users who will be harmed by not being able to 
read those files. Ultimately, they are more likely to turn their back at 
flowCore and stop using it rather than being able to convince instrument 
vendors to fix their software.

Cheers,
Josef

On 12-07-12 03:00 AM, bioconductor-request at r-project.org wrote:
> ------------------------------
>
> Message: 4
> Date: Wed, 11 Jul 2012 11:58:27 +0100
> From: David Corne<dwcorne at gmail.com>
> To:bioconductor at r-project.org
> Subject: [BioC] problems reading fcs files / flowcore / read.fcs
> Message-ID:
>          <CAFeka--GMXhzPib9SNWs1oFazAZrvtRSazwPtirTQsVuwnz79g at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Dears All,
>
> I find issues with being able to read FCS files using read.fcs from
> the flowcore package;
>
> So far it seems  FCS files from some instruments can't be read in R v
> 2.150 on either linux or windows, but with R V 2.13.0  and 2.14.0 they
> can be read in fine.
>
> It would be nice to be able to use the latest version of R - does
> anyone have a fix? Could the flowcore authors maybe release a new
> version where read.fcs works in R 2.15.0 ?
>
> VBD

-- 
Josef Spidlen, Ph.D.
Terry Fox Laboratory, BC Cancer Agency
675 West 10th Avenue, V5Z 1L3 Vancouver, BC, Canada
  
Tel: +1 (604) 675-8000 x 7755
http://www.terryfoxlab.ca/people/rbrinkman/josef.aspx