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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