Allison:
Your contrast looks correct. I have a set of test analyses and using a
contrast exactly as you describe below is perfectly valid. By the way I
assume you have n1+n2+2+3+6 columns in your design.
In any case inclusion of the main effects makes the design overly complex
and you can get similar results by only including the subject and
interaction effects. In that case your group contrast would be
ones(1,n1)/n1 -ones(1,n2)/n2 MEg zeros(1,nc) ones(1,nc)/nc -ones(1,nc)/nc
With respect to the roundoff errors, my guess is that this is to be
expected, although I know nothing about the algorithms for floating point
calculations. Attached is a plot of the rounding errors for every
combination of n1 and n2 from 1:100.
for n1 = 1:100
for n2 = 1:100
out(n1,n2)=sum([[ones(1,n1)/n1], [-ones(1,n2)/n2]]);
end
end
figure
surf(1:100,1:100,out)
shading interp
It makes a very pretty picture, and as you can see there is some type of
systematic variation in the roundoff errors that gradually increases as n1
and n2 increase. I don't know if this is related to floating point
calculations at the machine level or from matlab. The numbers vary between
-4.16e-015 to 4.13e-015. There are some actual zeros in the calulation, but
they don't have any obvious pattern. See the black and white figure.
Nevertheless, I don't think this is what is giving you the problem though as
the contrast works as noted above.
sorry not to be of more help.
darren
> -----Original Message-----
> From: Nugent, Allison C. (NIH/NIMH) [E] [mailto:[log in to unmask]]
> Sent: Tuesday, August 05, 2008 8:45 AM
> To: Darren Gitelman; [log in to unmask]
> Subject: RE: [SPM] correctly specifying repeated measures
> mixed model in SPM5
>
> It's still not working - I split this original post into two threads.
>
> I was originally trying to evaluate the full "main effect of
> group" contrast from page 10 of Jan's tutorial.
>
> Briefly, n1 and n2 are the N for groups 1 and 2 nc=num of
> conditions=2, ng=number of groups=2
> MEg=[1 -1]
>
> For a design matrix containing (in this order) subject
> effects, groups effects, condition effects, and
> group*condition interaction effects, the main effect of gruop
> contrast is:
>
> ones(1,n1)/n1 -ones(1,n2)/n2 MEg zeros(1,nc) ones(1,nc)/nc
> -ones(1,nc)/nc
>
> At one point I got this to work, but I only seem able to
> replicate failure and not success.
>
> I've tried just the first portion: ones(1,n1)/n1
> -ones(1,n2)/n2, which should be a valid contrast on its own,
> but I still get the "invalid contrast" message. And, when I
> sum the contrast in the matlab window, its close, but not
> equal to zero.
>
> In fact, even this:
>
> sum([ones(1,10)/10 -ones(1,4)/4])
>
> which should be evaluated to 0 without any problem with
> rounding erroris evauated as:
>
> -1.1102E-16
>
> Which makes me believe that something is seriously wrong with
> my matlab configuration. Has anyone seen this before?
>
> Allison
>
> -----Original Message-----
> From: Darren Gitelman [mailto:[log in to unmask]]
> Sent: Mon 8/4/2008 4:30 AM
> To: Nugent, Allison C. (NIH/NIMH) [E]; [log in to unmask]
> Subject: RE: [SPM] correctly specifying repeated measures
> mixed model in SPM5
>
> Allison
>
> This should work. It is close to eps (minimum number in
> Matlab). What contrast are you trying to set up and what is
> your design?
>
> Darren
>
> > -----Original Message-----
> > From: SPM (Statistical Parametric Mapping)
> [mailto:[log in to unmask]]
> > On Behalf Of Allison Nugent
> > Sent: Monday, August 04, 2008 2:08 PM
> > To: [log in to unmask]
> > Subject: Re: [SPM] correctly specifying repeated measures
> mixed model
> > in SPM5
> >
> > I think I spoke too soon regarding my success with getting symbolic
> > contrasts to work. At one point, I did manage to make this
> work, but
> > now,
> >
> > sum(ones(1,n1)/n1 -ones(1,n2)/n2)) = 9.43E-16
> >
> > instead of zero, which is exasperating! Is there something I can
> > change in my setup to fix this?
> >
> > Thanks!
> >
> > Allison
> >
>
>
>
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