[Bioc-devel] FCS3.0 DiVa files?

[Byron Ellis]

The data isn't mine so I'll have to ask. It's actually primarily for
quality control so it probably won't be a problem. Otherwise we'll
wait until I get to run my own data on the LSRII. :-)

On 9/6/06, Florian Hahne <f.hahne at dkfz-heidelberg.de> wrote:
> Hi Byron,
> do you think you could send me one of the diva files for testing
> purposes. I like to test against as many different file types as
> possible whenever I do changes to the import function and my supply is
> somehow limited to FACS Array and FACS Calibur files. By the way, FSC
> and SSC (and sometimes also other parameters) are viewed linearly
> because the amplification of the measured signals by the instrument is
> either linear or logarithmic, this can be set by the user. You can get
> the type of amplification for each parameter n from the $PnE keyword in
> the FCS file.
> Cheers,
> Florian
>
> Byron Ellis schrieb:
> > Actually, I stand corrected---I was looking at untransformed data and
> > comparing to transformed data (the Forward Scatter is usually viewed
> > linearly for whatever reason so it looked as it should). It looks like
> > the SVN version (as of today) reads the FACSDiVa files correctly.
> > Hooray. For the longest time it looked like there was an alignment
> > problem or something, but apparently not.
> >
> > Of course there are negative entries for values that are,
> > theoretically, photon counts but that's more the fault of the
> > equipment manufacturers who thought that hardware background
> > correction was a good idea. :-)
> >
> > P.S. Turning off a dump of the data matrix by default was a fantastic
> > idea. My test data is 13x~520K  and that just kills Aqua R.
> >
> > On 9/5/06, Wolfgang Huber <huber at ebi.ac.uk> wrote:
> >>
> >> Hi Byron,
> >>
> >> would it be possible to be more specific than "weird sorts of systematic
> >> errors", and for instance give some example files together with what you
> >> consider correct results?
> >>
> >>    Best wishes
> >>    Wolfgang
> >>
> >>
> >>
> >> Byron Ellis wrote:
> >> > The latest readFCS unfortunately doesn't produce sensible results
> >> > except for the first parameter (generally forward scatter), the other
> >> > parameters have weird sorts of systematic errors that almost look like
> >> > alignment problems. At least two other people in my lab here have Java
> >> > importers for these sorts of files that I'm considering to be
> >> > "correct" and working from there.
> >> >
> >> > On 9/4/06, Florian Hahne <f.hahne at dkfz-heidelberg.de> wrote:
> >> >> Hi Byron,
> >> >> As far as I know these files don't seem to adhere to the
> >> specifications
> >> >> in the FCS 3.0 format. I had one example file which I read in using a
> >> >> number of different software tools and almost all of them produced
> >> >> different results.
> >> >> readFCS could read the file without errors and the plots of the data
> >> >> looked ok. The only problem is that the absolute values are not
> >> the same
> >> >> for the different software, but the measurement relations are the
> >> same,
> >> >> i.e. the data is on different scales. And since I don't know what the
> >> >> correct values are (and are there "correct" values at all? In the end
> >> >> these are just arbitrary dimensionless numbers that somehow
> >> reflect the
> >> >> fluorescence intensities...) I didn't know how to proceed.
> >> >> Please feel free to take a stab at the import if you think that is a
> >> >> problem or send me one or two of your files along with some info
> >> about
> >> >> the expected range so I can give it another try.
> >> >> Cheers,
> >> >> Florian
> >> >>
> >> >> Byron Ellis schrieb:
> >> >>> Hi all,
> >> >>>
> >> >>> I remember a couple of months ago there was a brief discussion about
> >> >>> FCS3.0 files, in particular DiVA files recorded in floating
> >> point. Was
> >> >>> there ever any progress made on reading those in? I took a look
> >> >>> through the logs, but I may have missed something. I suddenly find
> >> >>> myself working with an LSR2 using DiVa that generates a lot of these
> >> >>> files. :-)
> >> >>>
> >> >>> If not, I'll take a stab at it since I need to read these files
> >> sooner
> >> >>> rather than later.
> >> >>>
> >> >>>
> >> >>
> >> >> --
> >> >> Florian Hahne
> >> >> Abt. Molekulare Genomanalyse (B050)
> >> >> Deutsches Krebsforschungszentrum (DKFZ)
> >> >> Im Neuenheimer Feld 580
> >> >> D-69120 Heidelberg
> >> >> phone: 0049 6221 424764
> >> >> fax: 0049 6221 423454
> >> >> web: www.dkfz.de/mga
> >> >>
> >> >>
> >> >
> >> >
> >>
> >>
> >
> >
>
>
> --
> Florian Hahne
> Abt. Molekulare Genomanalyse (B050)
> Deutsches Krebsforschungszentrum (DKFZ)
> Im Neuenheimer Feld 580
> D-69120 Heidelberg
> phone: 0049 6221 424764
> fax: 0049 6221 423454
> web: www.dkfz.de/mga
>
>


-- 
Byron Ellis (byron.ellis at gmail.com)
"Oook" -- The Librarian