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===Methylation marker selection=== *In this analysis, I tried to select a minimal subset of CpG sites that can classify the patients from the healthy controls at the greatest power. *Since there are too many sites in the data set, I decided to filter out most of the non-informative sites first, then use a feature selection method to identify a small subset of most informative markers. I did this with a [[Media:GA_methylation_MRMR_prep.txt|Perl script]] and [http://penglab.janelia.org/proj/mRMR mRMR]. **Step I: perform linear regression as previously, and only keep the sites with |t value|>2.5. **Step II: reformat the data in the right format, and perform feature selection with mRMR. **The output of mRMR is a list of 50 sites ranked based on a score ([[Media:KangZhang_GA_BSPP_95_MRMR_output.txt|mRMR output file]]). I then took the methylation data on these 50 sites, and did PCA analysis with R. Clearly patients and controls can be classified quite well based on the top 50 CpG sites. Even with the top 20 sites, the classification was still quite accurate. **[[Media:Gene_associated_with_top_50_markers.txt|Gene associated with the top 50 markers]]. [[Image:Classification_top_10_sites.png|1000px]] [[Image:Classification_top_20_sites.png|1000px]] [[Image:Classification_top_50_sites.png|1000px]]
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