On 22/08/2013 09:24, Sachinthaka Abeywardana wrote:
Hi all,
I get the expected behaviour of getting a useful model if I do the following
This is an 'expectation problem', not a 'stepAIC problem'.
And stepAIC is not part of R and you are not crediting the tools you use.
fit<-lm(
expressions[,i]~expressions[,pa_all[1]]+expressions[,pa_all[2]]+expressions[,pa_all[3]]+expressions[,pa_all[4]]+expressions[,pa_all[5]])
step<-stepAIC(fit, direction="both")
Output:
Step: AIC=-78.75
expressions[, i] ~ expressions[, pa_all[5]]
Df Sum of Sq RSS AIC
<none> 43.714 -78.750
+ expressions[, pa_all[4]] 1 0.83982 42.874 -78.690
+ expressions[, pa_all[2]] 1 0.80449 42.909 -78.608
- expressions[, pa_all[5]] 1 1.13431 44.848 -78.188
+ expressions[, pa_all[1]] 1 0.08445 43.630 -76.944
+ expressions[, pa_all[3]] 1 0.07620 43.638 -76.925
but if I do this instead, stepAIC isn't deleting any of the unwanted
columns. It seems to think it can only delete the entire set or none at all.
There is only one set to consider. You have a matrix as your single rhs
term. (We must guess: your code is incomplete and not reproducible.)
fit<-lm(expressions[,i]~expressions[,pa_all[1:5]])step<-stepAIC(fit,
direction="both")
Output:
Start: AIC=-74.42
expressions[, i] ~ expressions[, pa_all[1:5]]
Df Sum of Sq RSS AIC
- expressions[, pa_all[1:5]] 5 2.7111 44.848 -78.188
<none> 42.137 -74.424
Step: AIC=-78.19
expressions[, i] ~ 1
Df Sum of Sq RSS AIC
<none> 44.848 -78.188
+ expressions[, pa_all[1:5]] 5 2.7111 42.137 -74.424
Thanks,
Sachin
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Brian D. Ripley, rip...@stats.ox.ac.uk
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