[Bioc-devel] flowCore 1.22.0 broken for some FCS files (which it previously read without errors)

Steve Lianoglou mailinglist.honeypot at gmail.com
Thu Jun 14 01:09:39 CEST 2012

Hi Kieran,

I'm not really familiar w/ flowCore at all, but just wanted to note that:

On Wed, Jun 13, 2012 at 6:53 PM, Kieran O'Neill <koneill at bccrc.ca> wrote:
> It is also quite frustrating for me, in that no previous version of
> flowCore works in the current version of R (2.15.0), so I would need
> to downgrade the whole of R in order to downgrade to a working version
> of flowCore to analyse these files.

This isn't your only option -- you don't have to "downgrade" per se.
If you're really in pinch, you can install a previous version of R
*along side* your current install and simply install
biocLite('flowCore') to take a crack at your data.

In the best case, you could just save the binary file and reuse it in
a newer version of R/flowCore -- worst case is that you just run the
analysis on your older R install (I admit, not ideal but ... ).

Alternatively, if your input file isn't a binary one it probably
wouldn't be *too* cumbersome to debug what's causing the problem by
tracing through the offending function to whip up a fix, especially if
you have both versions of flowCore (new/broken and older/working) side
by side.

If it is binary, though, I can certainly appreciate how that might be
a stretch too far.


Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact

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