Noi/NOTES/2012-4-12: Difference between revisions

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>Noi
(Created page with "* To do list today ** continue mpo analysis --> convert tstat value to p-value by adding "pt($t_stat, $num_data-1)" and "use Math::CDF qw(pt);"to the script. Then perform mul...")
 
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* To do list today
* To do list today
** Have finished calculating FDR by BH correction and re-plot manhattan plots again. The results looked the same just change the p-value cutoff at FDR 10%.
** continue mpo analysis --> convert tstat value to p-value by adding  "pt($t_stat, $num_data-1)" and "use Math::CDF qw(pt);"to the script. Then perform multiple testing correction by multtest (R) to get q-value (BH FDR)
** continue mpo analysis --> convert tstat value to p-value by adding  "pt($t_stat, $num_data-1)" and "use Math::CDF qw(pt);"to the script. Then perform multiple testing correction by multtest (R) to get q-value (BH FDR)
** continue regression analysis --> do similar things to mpo analysis by editing script and correct multiple testing
** continue regression analysis --> do similar things to mpo analysis by editing script and correct multiple testing
** continue ASM analysis --> find FDR by printing out SNP-CpG ASM and p-value then perform multiple testing correction. Also need to find total number of tests.
** continue ASM analysis --> find FDR by printing out SNP-CpG ASM and p-value then perform multiple testing correction. Also need to find total number of tests.

Revision as of 23:14, 12 April 2012

  • To do list today
    • Have finished calculating FDR by BH correction and re-plot manhattan plots again. The results looked the same just change the p-value cutoff at FDR 10%.
    • continue mpo analysis --> convert tstat value to p-value by adding "pt($t_stat, $num_data-1)" and "use Math::CDF qw(pt);"to the script. Then perform multiple testing correction by multtest (R) to get q-value (BH FDR)
    • continue regression analysis --> do similar things to mpo analysis by editing script and correct multiple testing
    • continue ASM analysis --> find FDR by printing out SNP-CpG ASM and p-value then perform multiple testing correction. Also need to find total number of tests.