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Question: MSstats changes to dataprocess
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gravatar for nmay
8 months ago by
nmay0
nmay0 wrote:

Help! 

I'm revisiting some stats from an old MRM project (2014).  We uses MSstats with the help of the lab performing the proteomics work at the time, I have the R script and have updated it to get it working, however I think some of the defaults are different now and I can't reproduce the results in R. 

Is there any major differences than in skyline that I'm missing? Or differences in the dataprocess function?

Thanks!!

ADD COMMENTlink modified 8 months ago by mnchoi6740 • written 8 months ago by nmay0
1
gravatar for mnchoi67
8 months ago by
mnchoi6740
mnchoi6740 wrote:

- First, I recommend to check the version of MSstats you used. MSstats has big changes last couple of years. If you want to reproduce the results, you have to use the same version of MSstats.

- If you means, 'group comparison' option in Skyline, there are several major difference, like no imputation, different protein summarization and inference. If you means, 'MSstats external tool' in Skyline, it is the same as MSstats package.

- User manual at msstats.org(http://msstats.org/msstats-2/) show the options in dataProcess function for current version.

Hope to help.

- Meena

ADD COMMENTlink written 8 months ago by mnchoi6740
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