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

[Slebos, R. J. <Rob...@mo...>]

Hi Dave,
Nice code, ran perfectly!
I second Dan's consideration, especially where you link the quality
metrics to outcome (peptide counts etc.). There are biological
differences between the 95 samples and it is impossible to know how much
those affect your findings. It would be interesting to see how the
CompRef samples behave, the Sci Data paper has the assembly for all 32
CompRef runs we did during tumor and normal analyses. In my mind, the
question is still about how variability of the QC metrics matter for the
final product (good PSMs). Have you looked at what parameters determine
PC1, 2 etc?
Rob


On 10/18/2017 6:04 AM, David Tabb 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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-- 
-------------------------
Robbert Slebos, PhD
Senior Staff Scientist
Clinical Science Lab, MRC-2067B
Moffitt Cancer Center
13131 Magnolia Drive
Tampa, FL 33612

Tel: 813-745-3685
email: rob...@mo...
-------------------------

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