Re: [Psidev-qc-dev] Quality Control workshop for ClinProt 2017

[Daniel L. <dan...@pr...>]

Dave,

I’ll let the others respond on their own.  I have no real concerns.  You do suggest that an instrument becoming increasingly erratic with time could explain one of your observations.  I am confident that the data for the CompRef samples supports our assertion that the system was sufficiently stable to make reliable comparisons across runs and time.  This was a major element of the data analysis by Bing’s group.  However, nobody has looked at the data with a tool like this (although I’d bet Steve Stein has by now).  Although you explained your reasoning for not analyzing the CompRef data, that was nevertheless the main dataset through which we evaluated system stability over time.  It might be interesting to reconsider.

Dan

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Daniel C. Liebler, Ph.D. | President | Protypia, LLC 
9720 Turner Lane | Brentwood, TN 37027 | (615) 715-4312 
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On 10/18/17, 5:03 AM, "David Tabb" <dt...@su...> wrote:

    Hi, all!
    
    I am presenting a quality control workshop in Moscow on November 1st.  I
    am using the QuaMeter analysis of our 1425 CPTAC colon files from the
    attached paper by Rob Slebos (DOI 10.1038/sdata.2015.22) as a basis for
    this two-hour tutorial.  I have made some small edits to Xia Wang's R
    script for this purpose, and I have reconstructed the data files from
    which it was produced.  Today I have finished writing a Word document to
    guide people through the script to understand its operation.
    
    I hope you will have a chance to look through the attached files to see
    whether or not my Word document 1) reflects the technical principles
    correctly and 2) avoids casting aspersions in the data (I don't think
    the variation we saw across months of instrument operation was unusual
    or unexpected).  The presentation isn't until November 1st, so there's
    still time to make some corrections.
    
    I will have intermittent contact with the network during October
    19th-October 29th.
    
    Thanks,
    Dave
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