[R] Logistftest to select diagnostic genes

From: Lingsheng Dong <dong_lsh_at_hotmail.com>
Date: Thu 19 Jan 2006 - 04:14:18 EST


Hi, all,

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 expected.

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 dependent variable.
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 be appreciated.

Lingsheng

The fear of the LORD is the beginning of wisdom, and knowledge of the Holy One is understanding.
--Proverbs 10:10



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