[Bioc-devel] FCS3.0 DiVa files?
ellis at stat.harvard.edu
Wed Sep 6 04:46:22 CEST 2006
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
> 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
Byron Ellis (byron.ellis at gmail.com)
"Oook" -- The Librarian
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