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Hi again Gwenaëlle Many thanks, that's most helpful. Just finally - if you were a reviewer and saw just the three two-way comparisons, would you ask for the three-group analysis and post-hoc t-tests, or would you be happy with the three two-way analyses? Rgds Mark On 13/4/10 9:01 PM, "Gwenaëlle DOUAUD" <[log in to unmask]> wrote: > Hi Mark, > Thanks for your response - I guess I am interested in the > > result of an > F-test across the three samples so it sounds like it will > be > worth a try. Sure, but bear in mind that it will only tell you where are the > significant changes across the 3 groups, so you will still need to run the > post-hoc t-tests on each pair of groups to determine what's "driving" these > results. > With regards to what my question is: it's partially > answered by > my results > from the three 2-way analyses. I see that illness1 vs > controls > shows some > key reductions; illness2 vs controls shows more widespread > > reductions and in > larger clusters; illness1 vs illness2 shows no > differences > in either > direction. I'm interested in whether illness1 vs > illness2 > really differ, as > the separate comparisons against controls > implies that they > should, but a > direct comparison between them suggests > that they don't. Yes, it can happen, this means that though illness2 seems > more severe, this is not a significant effect. > (My numbers are > 20-30 in > each group). Does method II assist in this? There is no way of knowing for > sure, and if it does when you'll do the post-hoc t-test between illness1 and > 2, this would be just because you have increased your DoFs, not because you > would have asked a different question... Cheers, Gwenaelle > Rgds > > > Mark > > > On 13/4/10 4:20 AM, "Gwenaëlle DOUAUD" > <[log in to unmask]> > wrote: > > > Hi Mark and Jay, > > there is no > good answer to this question I'm afraid. > > Say > > you've got two subjects > in group A, 3 in B and 4 in C, > then both approaches > > are valid: > > > Method I > > A B > > 1 0 > 1 0 > 0 1 > 0 1 > 0 1 > for the design.mat of the > first > > A and B groups with > > 1 -1 (A-B) > -1 1 (B-A) > for the > design.con > and then repeat > > for groups B and C, then groups A and C > (which is what > you did Mark). > > Method > > II > > A B C > > 1 0 0 > 1 0 > 0 > 0 1 0 > 0 1 0 > 0 1 0 > 0 0 1 > 0 0 1 > 0 0 1 > 0 0 1 > for the > > > design.mat of the 3 groups with > > 1 -1 0 (A-B) > -1 1 0 (B-A) > 0 1 -1 > (B-C) > 0 -1 1 > > (C-B) > 1 0 -1 (A-C) > -1 0 1 (C-A) > for the design.con > (t-tests) > and > > 1 0 1 0 0 > > 0 > for the design.fts (F-test, as many > columns as there are > rows in your > > design.con, you just need to click in > "F-tests" in the > Glm gui and then click > > in front of the two relevant > "Contrasts" you have > already set up) > > So with > > Method II, you can > also ask the question of where are > the changes *across the > > 3 groups* > (F-test with the design.fts). You also get > an increase in DoF but, > > as > Tom Nichols said, if it happens that group C for > instance has wildly > > > smaller variance, you can get inflated significances > (or reduced power if > it > > has wildly larger variance). > > So it depends on what your main > question is, > > really. > > Hope this helps, > Gwenaelle > > > --- En date > de : Lun 12.4.10, Mark > > Walterfang <[log in to unmask]> > a > écrit : > > > De: Mark Walterfang > > <[log in to unmask]> > > Objet: > Re: [FSL] FSLVBM GLM Setup > > À: > > [log in to unmask] > > Date: Lundi 12 > avril 2010, 14h18 > > Hi all > > > > I'm in the > > same situation as Jay. I > have three groups > > (illness1, illness2 > > and > > controls), all matched > to each other. I've run three > > two-way analyses, > > > > which is pretty > laborious and I'm pretty sure it's > not > > statistically > > ideal. > > What > I can't work out is how to set up the design > matrices > > & > > contrasts > in > > the way Jay describes, as the online manual for > Randomise > > > > > doesn't really > > provide guidance here. Gwenaëlle, is this something > you > > > can > > advise on? > > > > Thanks in advance, > > > > Mark Walterfang > > > > > > > On 10/4/10 > > 12:29 PM, "Jay Ives" <[log in to unmask]> > > wrote: > > > > > > I have 70 subjects in > > 4 groups and would like to test > > between > individual > > > groups and > > combinations of the groups. Can someone > > > please advise me how to set > > > up > > the design.mat and design.con files > to do this? > > Thx > > > > > > WARNING: This > > message > > > originated > from outside the > Northern/Melbourne/Western > > Health > > e-mail network. > > > > The sender cannot be validated. Caution is > advised. > > > > Contact IT > Services (+61 3 > > > ) 9342 8888 for more information. > > > > > > > > > > > WARNING: This message originated from outside the > > > Northern/Melbourne/Western Health e-mail network. The > sender cannot be > > > validated. Caution is advised. Contact IT Services > (+61 3 ) 9342 8888 for > more > > information. > > > Dr Mark Walterfang > Consultant > Neuropsychiatrist > Neuropsychiatry Unit > Level 2, John Cade Building > ROYAL > MELBOURNE HOSPITAL 3050 AUSTRALIA > T +61-3-93428750 > F +61-3-93428483 > E > [log in to unmask] > W www.neuropsychiatry.org.au > > Research > Fellow > Melbourne Neuropsychiatry Centre > University of Melbourne > Level 2 > & 3, Allan Gilbert Building > 161 Barry St > CARLTON SOUTH 3023 AUSTRALIA > T > +61-3-83441800 > F +61-3-93480469 > E [log in to unmask] > W > www.psychiatry.unimelb.edu.au/mnc > WARNING: This message originated > from outside the Northern/Melbourne/Western Health e-mail network. The sender > cannot be validated. Caution is advised. Contact IT Services (+61 3 ) 9342 > 8888 for more information. -- Dr Mark Walterfang Consultant Neuropsychiatrist Neuropsychiatry Unit Level 2, John Cade Building ROYAL MELBOURNE HOSPITAL 3050 AUSTRALIA T +61-3-93428750 F +61-3-93428483 E [log in to unmask] W www.neuropsychiatry.org.au --