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

[Finak, Greg]

Hi, David
In 2.15 there were some changes to the FCS file reading routine to make it compliant with the FCS file standards (it was not compliant prior to 2.15, and led to other errors). Unforunately, the result was that FCS reading was broken (inadvertently) for files from instruments where the manufacturers were not following the standard (apparently there are a lot of manufacturers that don't bother to implement the standard correctly). We're working on correcting these errors as we get bug reports.

That said, it's next to impossible to help you out if you don't provide us with some more information.. i.e. provide a reproducible example,  sessioninfo(), the error message produced, and even an example of an FCS file where read.FCS fails.

We want to fix these issues for users, and we understand that having software suddenly break when it was fine one version ago can be frustrating, but complaining into thin air is not really productive for anyone. 

Best,

Greg Finak, PhD
Staff Scientist
Vaccine and Infectious Disease Division
Fred Hutchinson Cancer Research Center
Seattle, WA
gfinak at fhcrc.org
(206) 667-3116

> ------------------------------
> 
> 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