**From:** Liaw, Andy (*andy_liaw@merck.com*)

**Date:** Sat 15 May 2004 - 01:06:27 EST

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Message-id: <3A822319EB35174CA3714066D590DCD504AF7DA1@usrymx25.merck.com>

*>From the output you've shown, Minitab and R give the same thing when you ask
*

for the same thing. In Minitab,

*> Source DF Seq SS Adj SS Adj MS F P
*

*> sector 6 9.0605 2.9989 0.4998 1.21 0.297
*

*> depth 1 34.2072 11.9973 11.9973 29.16 0.000
*

*> sector*depth 6 1.5364 1.5364 0.2561 0.62 0.712
*

*> Error 578 237.7830 237.7830 0.4114
*

*> Total 591 282.5871
*

In R:

*> Response: Expr1
*

*> Df Sum Sq Mean Sq F value Pr(>F)
*

*> sector 6 9.1 1.5 3.67 0.0014 **
*

*> depth 1 34.2 34.2 83.15 <2e-16 ***
*

*> sector:depth 6 1.5 0.3 0.62 0.7124
*

*> Residuals 578 237.8 0.4
*

Note the R output matches the `Seq SS' in Minitab, because that's what R

says it does: sequential tests. By `Adj. SS' and associated tests, I guess

Minitab meant `adjusting for other terms in the model'. If so, use drop1().

HTH,

Andy

*> From: mrufino@cmima.csic.es
*

*>
*

*> Dear R list,
*

*>
*

*> I have been trying to do a linear model, extracting the effect of a
*

*> covariate.... and the results do not match, when I do it with
*

*> other programs
*

*> (e.g. minitab).... so it is obvious that I was doing something wrong.
*

*>
*

*> Whan I do it with minitab, I have this results: (sector is a
*

*> factor and depth
*

*> is the covariate):
*

*>
*

*> Source DF Seq SS Adj SS Adj MS F P
*

*> sector 6 9.0605 2.9989 0.4998 1.21 0.297
*

*> depth 1 34.2072 11.9973 11.9973 29.16 0.000
*

*> sector*depth 6 1.5364 1.5364 0.2561 0.62 0.712
*

*> Error 578 237.7830 237.7830 0.4114
*

*> Total 591 282.5871
*

*>
*

*>
*

*> If I do with R, I have been trying everything it occurrs to
*

*> me and looked
*

*> everywhere and I could not obtain the same results and
*

*> nothing is clear to
*

*> me... (I am so sorry... probably it is lack of statistical knowledge):
*

*>
*

*> If I do:
*

*> > anova(lm(Expr1~depth*sector))
*

*> Analysis of Variance Table
*

*>
*

*> Response: Expr1
*

*> Df Sum Sq Mean Sq F value Pr(>F)
*

*> depth 1 38.2 38.2 92.76 <2e-16 ***
*

*> sector 6 5.1 0.9 2.07 0.055 .
*

*> depth:sector 6 1.5 0.3 0.62 0.712
*

*> Residuals 578 237.8 0.4
*

*>
*

*> I am simply fitting a crossed anova, or because depth is
*

*> continuos ... what is
*

*> it doing?
*

*>
*

*> then, as it was not right, I went to look in the manuals, and in 'an
*

*> introduction to R' states:
*

*> y ~ A + x Single classification analysis of covariance model
*

*> of y, with classes
*

*> determined by A, and with covariate x. Is it like this?
*

*> > anova(lm(Expr1~sector+depth)) #I don't think so...
*

*>
*

*> But I interpreted this as a additive model... and besides it
*

*> did not work as
*

*> well, so I tried what a friend recomended, i.e. x:z, whereas
*

*> we are extacting
*

*> the effect of x (covariate) on y... but it does not work as well...
*

*> > anova(lm(Expr1~sector+depth+depth:sector)) # Would it be like this?
*

*> Analysis of Variance Table
*

*>
*

*> Response: Expr1
*

*> Df Sum Sq Mean Sq F value Pr(>F)
*

*> sector 6 9.1 1.5 3.67 0.0014 **
*

*> depth 1 34.2 34.2 83.15 <2e-16 ***
*

*> sector:depth 6 1.5 0.3 0.62 0.7124
*

*> Residuals 578 237.8 0.4
*

*> -
*

*> or like: anova(lm(Expr1~depth:depth*sector))
*

*>
*

*>
*

*> I am lost... in the other times I just did with minitab, but
*

*> I realy wanted to
*

*> do it with R... can someone give me some lights?
*

*> Is it very difficult to do it with R?
*

*> Sorry for the long and messy email,
*

*>
*

*> thank you very much in advance,
*

*> Marta
*

*>
*

*> ______________________________________________
*

*> R-help@stat.math.ethz.ch mailing list
*

*> https://www.stat.math.ethz.ch/mailman/listinfo/r-help
*

*> PLEASE do read the posting guide!
*

*> http://www.R-project.org/posting-guide.html
*

*>
*

*>
*

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