[R] Logistftest to select diagnostic genes
dong_lsh at hotmail.com
Wed Jan 18 18:14:18 CET 2006
Anyone has experience on Logistf package? I am using logistftest in Logistf
package to selelct diagnosis genes. The result seems not the same as I
I have 10 gene expression data for 27 tumor 1 and 11 tumor 0. I want to
select the best one using Maximum likelihood ratio test in logistic
regression model. This is the way my code works:
1. Read in 10 genes as independent variables and tumor type (1 or 0) as
2 Fit in a 10 variable logistic model and calculate it's likelihood.
3 Loop through the 10 genes, each time take one gene out of the model and
calculate the likelihood without the gene. And compare each new likelihood
with the likelihood of the original original 10 variable model to get
likelihood ratio test for each gene.
I guess gene 8 should have best discrimination power because it can totally
seperate the two group tumors. But the test result shows the likelihood
ratio for Ratio 8 is not the biggest.
Where am I wrong? The package is not good for this problem? But the package
document says this package takes care of separation and small sample size by
finite parameter estimates and profile penalized log likelihood. Or my
assumption is wrong? I am totally lost.
Thank you very much for reading this email! Your suggestion or comments will
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