[RASMB] error estimates and F-statistics in Sedphat

[John J. Correia]

Mark

Not clear how you get s1 and s2 from a single sample analysis for an interacting system? If cs gives you two peaks its because the trailing edge of a monomer dimer reaction boundary gets turned into a peak. But its not a species if its truly an interacting system. You must do a wide concentration range, show a shift in Sw and extrapolate the end points. Then choose a model and fit to it.


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From: rasmb-bounces at rasmb.bbri.org [rasmb-bounces at rasmb.bbri.org] On Behalf Of Mark Agacan [M.Agacan at dundee.ac.uk]
Sent: Tuesday, April 26, 2011 10:36 AM
To: RASMB at rasmb.bbri.org
Subject: Re: [RASMB] error estimates and F-statistics in Sedphat

Thanks Patrick and Chad for the information about error estimates from F-statistics.

My problem now is that the apparent errors for the binding constants derived from the analysis of F-statistic appear to be very large.  When I make a change to e.g. log10Ka12, by any value from 0.1 - 3.0, there is no change (or only a very small change) in chi squared, so I can never reach the critical chi squared.

Each dataset looks good and gives low rmsd values when processing with the c(s) model in sedfit.  I'm using the monomer-dimer self-association model in sedphat, with the values for S1 and S2 taken from c(s) analysis.  I have tried to fit to other models with only worse results.

The fit looks very poor (see screenshots attached).  I don't think I need to repeat the experiment because the data looks good, at least to my eye, but the fit to the monomer-dimer model seems very bad.

Any further suggestions or advice would be very welcome.

Many Thanks,

Mark




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Dr Mark Agacan, Scientific Officer for the Division of Biological Chemistry and Drug Discovery,
Wellcome Trust Biocentre, College of Life Sciences, University of Dundee, Dundee, DD1 5EH
Tel: +44 1382 386095    Fax: +44 1382 345764    Mobile: 07525 451 117
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>>> Chad Brautigam <Chad.Brautigam at UTSouthwestern.edu> 4/23/2011 15:02 >>>
Hi, Mark,

The F-statistics in SEDPHAT are meant to allow you to construct a "do-it-yourself" error interval.  Check out the statistics help page.  Under the heading "Error Analysis" there is a procedure for how to use the output "critical chi-square" from the Statistics Menu to find an error interval.

Cheers,
Chad

________________________________
From: rasmb-bounces at rasmb.bbri.org [rasmb-bounces at rasmb.bbri.org] on behalf of Mark Agacan [M.Agacan at dundee.ac.uk]
Sent: Friday, April 22, 2011 6:36 AM
To: rasmb at rasmb-email.bbri.org
Subject: [RASMB] error estimates and F-statistics in Sedphat

Hello,

I'm calculating errors in the binding constants in sedphat as instructed in the statistics help page, but I don't appear to get an output for the F-statistics.  Are the F-stats output only as (changes in) chi-squared values? e.g. the error associated with the binding constants is clearly given in the covariance matrix.

Best Wishes,

Mark


~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Dr Mark Agacan, Scientific Officer for the Division of Biological Chemistry and Drug Discovery,
Wellcome Trust Biocentre, College of Life Sciences, University of Dundee, Dundee, DD1 5EH
Tel: +44 1382 386095    Fax: +44 1382 345764    Mobile: 07525 451 117
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~


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