User: anamaria

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anamaria100
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Posts by anamaria

<prev • 130 results • page 1 of 13 • next >
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Comment: C: Why different reference panels change the signal for a SNP?
... Thanks for the link. Yes I understood that the power to detect the low frequency SNPs increases...HRC panel has much more SNPs and is done on immensely more subjects. I also did a plot to compare my imputed data with HRC ("new") with imputed data for HapMap2 ("old") and indeed that is the case. Also ...
written 3 hours ago by anamaria100
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Why different reference panels change the signal for a SNP?
... Hello, can someone please explain to me why here for fig 2 https://www-nature-com.proxy.cc.uic.edu/articles/ng.3643/figures/2 signal for this SNP changes between different versions of reference panels. In particular in between HapMap 2 and HRC? Here is a description of those two panels:https://im ...
hapmap hrc imputation referencepanel written 10 hours ago by anamaria100 • updated 4 hours ago by curious440
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Comment: C: Difference in imputation between platforms and RS names
... Yes indeed. Unfortunately I don't have any record on what kind of MAF threshold was used prior and post imputation in 2011. What number for MAF would you suggest me to impose on the new dataset judging by the old data? Should I do MAF 0.1 on both genotypes prior to doing regression analysis in plink ...
written 4 days ago by anamaria100
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Comment: C: Difference in imputation between platforms and RS names
... it seems that characteristics of overlapping SNPs is that there is not many of them who have very low minor allele frequency. Attached is the plot for frequencies for overlapping SNPs. Any idea why this might be? https://imgur.com/XkCxpvz https://imgur.com/cWfsHxu ...
written 4 days ago by anamaria100
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Comment: C: Difference in imputation between platforms and RS names
... I completely understand you. And I already confirmed analysis I did in 2020 in other known GWAS results (doing the most recent QC steps, methods...). But we need to know why 2011 was so different. ...
written 4 days ago by anamaria100
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Comment: C: Difference in imputation between platforms and RS names
... I don't have log files for 2011 data. What about comparing F_A Frequency of this allele in cases and F_U Frequency of this allele in controls. What would this be indication of? https://imgur.com/JoFtE6P https://imgur.com/53yGfNh ...
written 4 days ago by anamaria100
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Comment: C: Difference in imputation between platforms and RS names
... what about SNPs like this: rs2905035, rs2519016...which can be found in 2011 imputation bot not in 2020 ...
written 4 days ago by anamaria100
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Comment: C: Difference in imputation between platforms and RS names
... HI Kevin, I did match based on RS name, not on position. Do you advise me matching based on position? ...
written 4 days ago by anamaria100
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Difference in imputation between platforms and RS names
... Hello, so I have SNPs (RSIDs) from imputation done in 2011 on http://csg.sph.umich.edu/abecasis/MACH/tour/ (call it 2011 data) and I did imputation on the same genotype files on Michigan Imputation Server, Genotype Imputation (Minimac4) 1.2.4 (call it 2020 data) using the same QC steps I perfomed ...
rs minimac snps imputation mach written 5 days ago by anamaria100 • updated 4 days ago by Kevin Blighe65k
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Comment: C: PLINK logistic regression analysis and covariates
... Hi Kevin, I did run GWAS with and without TD covariate and p values appear to be highly correlated: data: tt$P_TD and tt$P_noTD t = 20.17, df = 283, p-value < 2.2e-16 alternative hypothesis: true correlation is not equal to 0 95 percent confidence interval: 0.7156134 0.8117108 sample estimate ...
written 8 days ago by anamaria100

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