[GET-Editors] Editing questions

[Kimberly Robasky]

On Wed, Oct 13, 2010 at 3:20 PM, Madeleine Price Ball <meprice at gmail.com>wrote:

> On the same example, how do I calculate the case/controls 'significance'?
>
> We've been using a two-tailed Fisher's Exact test. You can find some
> calculators online, for example:
> http://www.graphpad.com/quickcalcs/contingency1.cfm
> Each box in this is case+, case-, control+, control-, accourding to
> your data (28, 338, 50, 2320) this is < 0.0001.
>
> To get odds ratio (OR): (28 / 338) / (50 / 2320) = 3.84
>
> That puts SLC45A2-E272K at four stars based on the data from Graf et
> al you recorded, according to the current criteria.
>

Is there anything to keep us from building that calculation into
GET-Evidence?  It seems to me that by querying the user to input it by hand
only invites human error.  Would it make sense to supercede human entries
for this number later, when we implement the significance and OR
calculations?


>
> >  How do I calculate familial LOD score?
>
> This is complicated -- first you'll need a pedigree. I mean to write
> up a guide on it, although I'm still not totally confident that I
> understand it correctly. Sometimes a paper mentions LOD, in which case
> you can use that. If there aren't pedigrees (for example, everything
> is case/control data) then familial evidence is zero stars.
>

Again - wonder how much can be automated.

>
>  -- Madeleine
>
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