Post by emmao on May 3, 2016 12:55:09 GMT
Hello,
I'm new to data analysis and I'm having some trouble understanding the process and need help with a few questions.
I am running a conditional analysis on chromosome 19 in relation to Alzheimer's disease, I understand that conditional analysis tests whether SNPs have association independent of the SNP/SNPs you're conditioning for.
I started by running logistic regression on my whole dataset of ~529'000 SNPs and the top SNP belonged in chr 19. I ran the conditional analysis conditioning for this top SNP and results gave the majority of the SNPs p<10x5^-8 (my genome wide significant threshold). My supervisor explained that this is due to the highly associated APOE region and suggested focusing my conditional analysis on chromosome 19.
I have run the conditional analysis again on my ~9500 SNPs from chr 19, I have read that you continue to add SNPs from the results to the list of SNPs you are conditioning for and re-running the analysis until the results are no longer genome wide significant. This I understand yields secondary signals?
So far I have done the above 33 times and still the large majority of results from the cma.cojo file are genome wide significant, do I just carry on? as it seems like there will be many hundreds more to add. Are the SNPS that are genome wide significant independent from my top SNP?
Also the test gives me a given.cojo file with the SNPs I've conditioned for and various statistics including a p-value, I have noticed that the p-value of many of the 33 SNPs are no longer have a genome wide significant p-value, what is this file suppose to show?
Many Thanks,
Emma
I'm new to data analysis and I'm having some trouble understanding the process and need help with a few questions.
I am running a conditional analysis on chromosome 19 in relation to Alzheimer's disease, I understand that conditional analysis tests whether SNPs have association independent of the SNP/SNPs you're conditioning for.
I started by running logistic regression on my whole dataset of ~529'000 SNPs and the top SNP belonged in chr 19. I ran the conditional analysis conditioning for this top SNP and results gave the majority of the SNPs p<10x5^-8 (my genome wide significant threshold). My supervisor explained that this is due to the highly associated APOE region and suggested focusing my conditional analysis on chromosome 19.
I have run the conditional analysis again on my ~9500 SNPs from chr 19, I have read that you continue to add SNPs from the results to the list of SNPs you are conditioning for and re-running the analysis until the results are no longer genome wide significant. This I understand yields secondary signals?
So far I have done the above 33 times and still the large majority of results from the cma.cojo file are genome wide significant, do I just carry on? as it seems like there will be many hundreds more to add. Are the SNPS that are genome wide significant independent from my top SNP?
Also the test gives me a given.cojo file with the SNPs I've conditioned for and various statistics including a p-value, I have noticed that the p-value of many of the 33 SNPs are no longer have a genome wide significant p-value, what is this file suppose to show?
Many Thanks,
Emma