User: charvinangia

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charvinangia30
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Posts by charvinangia

<prev • 15 results • page 1 of 2 • next >
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Comment: C: Post PCA analysis
... Yes, the results are different. Okay, will try out your step 3. Thanks! ...
written 4 days ago by charvinangia30
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Comment: C: Post PCA analysis
... The overall aim is to identify age at diagnosis of diabetes in 2 populations. 1.I did a GWAS for age at diagnosis for the first population. 2.Next, I merged the data of the 2 populations and did a PCA on them. I got 2 different clusters. 3.Next, I was asked to run a GWAS using the first PC as a p ...
written 4 days ago by charvinangia30
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Comment: C: Post PCA analysis
... So I did a GWAS using the first principal component as a phenotype and plotted a manhattan plot. I got a few hundred hits (above the 5* e -8) Is that normal? My next step would be to use the top hits as covariates for the GWAS on my main phenotype. ...
written 4 days ago by charvinangia30
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Comment: C: Post PCA analysis
... Beautiful! Thank you so much Kevin! It has been of immense help. ...
written 7 days ago by charvinangia30
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Comment: C: Post PCA analysis
... By running a GWAS on the 2 merged populations A and B, I will be using the first principal component as a phenotype. Will that give me information about which principle component belongs to which population? ...
written 8 days ago by charvinangia30
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Comment: C: Post PCA analysis
... Thank you once again Kevin! ...
written 8 days ago by charvinangia30
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Comment: C: Post PCA analysis
... Thanks Kevin! I have one more question ...may sound a bit silly. Does it make sense to use the principle component as a phenotype in GWAS? ...
written 9 days ago by charvinangia30
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Comment: C: Post PCA analysis
... Data set B was pruned based on Linkage diseuqilibrium using the --indep-pairwise option in Plink. However, if I did pruning in A, it was removing most of the SNPs. Hence, I merged A as a whole (without pruning) to a pruned B and ran a PCA. My aim was to merge A and B (which are very different popula ...
written 10 days ago by charvinangia30
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Post PCA analysis
... Hello, I have data of two different populations - A and B. I merged both the data sets (unpruned A and LD pruned B) and did a PCA. I got two different clusters. Next, I'm supposed to identify the principle components that separate A and B, then take the A selective principle components and run a GW ...
population stratification pca correlation matrix written 10 days ago by charvinangia30 • updated 8 days ago by Kevin Blighe39k
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Comment: C: Problems with PCA for genotyped data
... Thank you so much Kevin! An --indep-pairwise cutoff of 1000 5 0.2 worked! Sorry, I couldn't reply yesterday due to the messaging limit for new users. ...
written 14 days ago by charvinangia30

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