# [R] Help - lm, glm, aov results inconsistent with other stati stical package

Liaw, Andy andy_liaw at merck.com
Wed Mar 1 02:14:57 CET 2006

```1. You have levels(A) as "2" and "4", yet you showed equations for A=0 and
A=1?

2. y = A + X + A*X means you're allowing the different groups of A to have
different slopes.  Probably not what you intended.

3. It's probably best to provide a small sample of the data (and R code) so
we know how you got what you got.

Andy

From: Ben Ridenhour
>
> Hello,
>
>  I 'm sure there must a be a simple explanation for what I'm
> doing wrong but I am stumped.  I am a novice R user and this
> has shaken my confidence in what I'm doing! I am trying to
> run a simple ANCOVA using the model y~A*x, where y and x are
> continuous and A has two levels.  Everything seems fine until
> I compare the output with what I get from another statistical
> package (JMP).  JMP has the model y=A+x+A*x (this should be
> the same as what I specified to R, correct?).  In comparison
> I get the line equations
>
>  y = 7072.09-1024.94 x (for A=0) and
>  y = 7875.58-970.088 x (for A=1)
>
>  from JMP.  And from R I get
>
>  y = 6276.7-1259.8 x (for A=0) and
>  y = 7867.5-1150.1 x (for A=1).
>
>  Obviously, these aren't even close to the same answer.  I've
> tried this using glm(), lm(), and aov() and as expected they
> all give the same answer.  If I do
>
>  >levels(A)
>  [1] "2" "4"
>
>  which are the two levels of A.  Why can't I get the same
> answer from JMP as in R?  This is very disturbing to me!
>
>  Thanks,
>  Ben
>
>
> -------------------------------
> Benjamin Ridenhour
> School of Biological Sciences
> Washigton State University
> P.O. Box 644236
> Pullman, WA 99164-4236
> Phone (509)335-7218
> --------------------------------
> "Nothing in biology makes sense except in the light of evolution."
> -T. Dobzhansky
>
>
>
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