Re: [Psidev-ms-dev] binaryArrayData lengths

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I also think that opening the door to arrays of differing lengths is a
complexity is best not done at this time.

Any additional arrays that I can think of, S/N or charge or similar
could all have the same number of elements. Yes, I suppose I could
imagine having something like:

m/z axis 1

intensity values corresponding to axis 1

m/z axis 2 for a subset of points in axis 1

charge values for axis 2

But I think that this is complexity that we have survived thus far
without and we best leave out at this point.

So, I propose we limit all binaryDataArrays lengths within one
<spectrum> to be the same.

Any dissent? Please provide a specific example of XML you'd like to see
instead.

Thanks,

Eric

________________________________

From: psi...@li...
[mailto:psi...@li...] On Behalf Of Angel
Pizarro
Sent: Tuesday, February 12, 2008 4:42 PM
To: Mass spectrometry standard development
Subject: Re: [Psidev-ms-dev] binaryArrayData lengths

On Feb 12, 2008 5:46 PM, Brian Pratt <bri...@in...> wrote:

	I think that's not quite right - arrayLength needs to remain an
attribute of
	BinaryDataArray since not all BinaryDataArray elements in a
spectrum will
	necessarily contain the same number of entries as an mz or
intensity array,

 Such as .... ?  I asked for examples of this and never got a reply. 

Related question, if they are different lengths how would you go about
assigning a value to a particular index (or set of indexes) that the
value refers to in another binary array?

 My point is that it would be infinitely easier to just repeat values
(MRM transitions values, retention time values, or even nil values) that
pertain to more than one index so you always have a 1:1 correspondence
across arrays. Of course I am making the assumption that all binary
arrays within a single spectrum element are related to each other in
some manner, so if this does not hold true, please someone tell me, as I
am fairly ignorant on the mass spec acquisition modes. 

The alternative representation would be coordinate systems and
multidimensional data arrays a la netcdf or HDF5,  but we are too far
along the route that we have laid out to even consider a change this
radical. BTW, I did do some mzData  (v 1.05) to netcdf conversion and
the netcdf files are even bigger, at a gain of built in index into the
data arrays within and across spectra. 

-angel

	since not all BinaryDataArray elements are guaranteed (as I
understand mzML,
	which is but dimly) to be mz or intensity.  You'll need to write
it again as
	an attribute of spectrum, something like mzintPairsCount if you
don't like
	PeaksCount.

	-----Original Message-----
	From: psi...@li...

	[mailto:psi...@li...] On Behalf
Of Eric
	Deutsch
	Sent: Tuesday, February 12, 2008 1:28 PM
	To: Mass spectrometry standard development

	Cc: Eric Deutsch
	Subject: Re: [Psidev-ms-dev] binaryArrayData lengths

	So there seems to be broad consensus (4 for 4;) that moving the
	arrayLength up a little higher is a good idea.  So instead of:

	<spectrum id="S19" scanNumber="19" msLevel="1">
	       <spectrumDescription>
	               ...
	       </spectrumDescription>
	       <binaryDataArray arrayLength="1313" encodedLength="5433"
	dataProcessingRef="Xcalibur Processing">
	               ...
	               <binary>AAAAwDsGeUAAAAD...</binary>
	       </binaryDataArray>
	       <binaryDataArray arrayLength="1313" encodedLength="4892">
	               ...
	               <binary>AAAAAIBJxk...</binary>
	       </binaryDataArray>
	</spectrum>

	We will have:
!!!!!!!!!!!!!!!!!!

	<spectrum id="S19" scanNumber="19" msLevel="1"
arrayLength="1313">
	       <spectrumDescription>
	               ...
	       </spectrumDescription>
	       <binaryDataArray encodedLength="5433"
	dataProcessingRef="Xcalibur Processing">
	               ...
	               <binary>AAAAwDsGeUAAAAD...</binary>
	       </binaryDataArray>
	       <binaryDataArray encodedLength="4892">
	               ...
	               <binary>AAAAAIBJxk...</binary>
	       </binaryDataArray>
	</spectrum>

	Agreed?

	> -----Original Message-----
	> From: psi...@li...
	[mailto:psidev-ms-dev-
	> bo...@li...] On Behalf Of Matthew Chambers
	> Sent: Wednesday, February 06, 2008 10:49 AM
	> To: Mass spectrometry standard development
	> Subject: Re: [Psidev-ms-dev] binaryArrayData lengths
	>
	> I agree that the primary data arrays should probably be
treated as
	> special in the schema so it's clear that they are paired
values and
	thus
	> peak count could move into the spectrum element or
	spectrumDescription.
	> There should still be options to have additional arrays that
aren't
	the
	> same as the main arrays (for example, an additional set of
arrays, one
	> for a subset of the m/zs and the other for peak charge
information).
	>
	> -Matt
	>
	>
	> Kessner, Darren E. wrote:
	> > Any other comments regarding <binaryArrayData> lengths?
	> >
	> >
	> >> (from Rune)
	> >> If they have to be equal size, then
	> >> that size ought to be specified in the spectrumDescription.
	> >>
	> >
	> > I agree -- I would like to encode the length in <spectrum>
somewhere
	> > (either attribute or cvParam) so that:
	> > 1) it's clear that the arrays are of equal size
	> > 2) Readers don't have to peek into the attributes of the
first
	> > <binaryArrayData> to get the info
	> >
	> > I need this right now for the MSData RAMP adapter code, so
I'll
	encode
	> > it as a <userParam> until a decision has been made on the
	specification.
	> >
	> >
	> > Darren
	>
	>
	>

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-- 
Angel Pizarro
Director, ITMAT Bioinformatics Facility
806 Biological Research Building
421 Curie Blvd.
Philadelphia, PA 19104-6160
215-573-3736 