User: maya123z
maya123z • 30
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Posts by maya123z
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... Thank you for the detailed answer! I'm curious, how trustworthy can we consider the odds ratios in this paper, considering they don't seem to be correcting for any covariates? ...
written 9 months ago by
maya123z • 30
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... I am reading a paper ([link here][1]) where they did a GWAS looking for Alzheimer's-associated genes. In their Table 2, a lot of the associated SNPs have an odds ratio that's less than 1. Does that mean that the minor allele is protective against Alzheimer's? Or, is this just because these are raw o ...
written 9 months ago by
maya123z • 30
• updated
9 months ago by
Kevin Blighe ♦ 35k
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... I recently ran a GWAS in GEMMA to fit a linear mixed model and generate p-values using the likelihood ratio test. I've identified 20 SNPs that are statistically significant. The output file just includes the following columns: SNP ID, chromosomal position, number missing in my dataset, major allele, ...
written 9 months ago by
maya123z • 30
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... See my responses to Kevin above. I pre-filtered my genotype data by maf > 1% and missingness <15%. ...
written 9 months ago by
maya123z • 30
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... Update: The results from using 2 PCs look basically the same. Unfortunately I think I'm probably just going to have to note the likely existence of bias in my data due to the experimental design. For the purposes of my undergraduate thesis at least, this will not be a major problem. Thanks to both o ...
written 9 months ago by
maya123z • 30
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... Here's what the QQ plot looks like for the Wald test when including 5 PCs: https://imgur.com/a/KjMV6 It's still not great but a bit better, though the p-values are quite a bit larger. I'll give it a try with fewer PCs and let you know the results... ...
written 9 months ago by
maya123z • 30
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... Yes, they seem to all be around 0.25-0.35. I tried it without the PCs included as covariates, but as the original post states, this caused the resultant QQ plot to have a strange wavy-looking shape, and I'm not sure why. ...
written 9 months ago by
maya123z • 30
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... I am currently working on running a GWAS using GEMMA to apply a linear mixed model, and I've been experiencing some difficulties with my analysis. Specifically the QQ plot has shown some early deviation from the expected line, as I described in a [previous question][1]. I also recently noticed that ...
written 9 months ago by
maya123z • 30
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... Since none of the pc's or other covariates were statistically significant, I ran the analysis again without any covariates. The QQ plot from that data had a strange step-shaped pattern: https://imgur.com/a/t9Zu7 ...
written 9 months ago by
maya123z • 30
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... Ah I see. That's strange because for all other papers I've seen using this model set (205 inbred Drosophila lines derived from the same geographical area) always include 5-20 principle components as covariates. In my case, I fitted a logistic regression to the first 5 pc's and determined that none w ...
written 9 months ago by
maya123z • 30
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9 months ago,
created an answer that has been accepted.
For A: How to input covariates in GEMMA?
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