Re: [Psidev-ms-dev] binaryArrayData lengths

[Randy J. <rkj...@in...>]

I also agree that there is no problem with moving the array length up.  

 

I would like to ask again:

 

1.	is scanNumber different from <scan> which lives lower
2.	can we make msLevel either optional, or a cvParam?

 

Randy

 

________________________________

From: psi...@li...
[mailto:psi...@li...] On Behalf Of Angel
Pizarro
Sent: Tuesday, February 12, 2008 4:34 PM
To: Mass spectrometry standard development
Subject: Re: [Psidev-ms-dev] binaryArrayData lengths

 

+1 agreed 

-angel

On Feb 12, 2008 4:27 PM, Eric Deutsch <ede...@sy...>
wrote:


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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