Hi all,
I get the expected behaviour of getting a useful model if I do the following
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.
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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