User: viavialin

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viavialin70
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Canada
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1 year, 10 months ago
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7 years, 2 months ago
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Posts by viavialin

<prev • 14 results • page 1 of 2 • next >
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Comment: C: Mapping SNPs with just position from ATG on gene
... Thanks for the suggestion, I eventually remapped the coordinates on the old version hg16 and used Kaviar to identify closest SNPs based on my converted input coordinates.  ...
written 6.2 years ago by viavialin70
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Comment: C: Mapping SNPs with just position from ATG on gene
... Unfortunately, I do not have the rs IDs! In fact, I am trying to identify the rs# from this paper.. ...
written 6.2 years ago by viavialin70
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Mapping SNPs with just position from ATG on gene
... I'm trying to annotate the SNPs (ie. the rs# and chromosome position) from this Table 1 in this paper but am having difficulty locating the SNPs on the gene. This table describes the position of each SNP from the ATG and I have identified the ATG to be chr3:183,732,180 (GRCh37) for NM_005688. Since ...
snps rs# written 6.2 years ago by viavialin70 • updated 6.2 years ago by Devon Ryan97k
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Significance of PLINK epistasis p-values
... I performed an epistasis analysis on PLINK using the following options-   --epistasis --epi1 1   The output from PLINK reports tests significant at a p-value (asymptotic p-value) <1e-4 by default. Since I am not performing a GWAS and I only have 400 SNPs, I changed the output to include all ...
epistasis plink p-values written 6.3 years ago by viavialin70 • updated 5.1 years ago by Biostar ♦♦ 20
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Answer: C: Haplotype construction based on SNPs with haploview
... For your purpose, I think that the Linkage Format would be the best. I have done similar analysis using both Linkage Format and HapMap Format.    Data file : Should be in the format - Ped ID, Indiv ID, Father ID, Mother ID, Sex, Outcome, x2 Alleles. (as described in the link provided above Locus ...
written 6.4 years ago by viavialin70
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Calculating association with outcome variable and Phased Haplotypes
... I am trying to determine association between a set of haplotypes (2 or 3 marker SNPs) with a clinical outcome. I have phased the haplotypes using Phase v2.1.1 and calculated OR, p values using a 2x2 Fisher's exact test.  My supervisor says that I should be considering the reference haplotype (major ...
haplotypes phasing written 6.4 years ago by viavialin70
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Answer: A: P Values In Plink
... I use --logistic with --covar .txt and --covar-name multivariate analysis. I do not use --adjust. Should I be using it? I am comparing the p values for 400 SNPs vs 70 SNPs with the same commands (logistic + covar) and I get different p values, slightly different ORs for the same SNPs. I tried doi ...
written 6.8 years ago by viavialin70
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P Values In Plink
... I have a simple question about the OR and p values derived from PLINK analysis (with covariates using --logistic and --covar) Does it make sense that the OR and p values change when I use different number of SNPs for a Fisher's Exact Test? The OR values are not too different but the p values ofte ...
snps plink written 6.8 years ago by viavialin70
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Comment: C: Fdr Q Values Calculations Using Q-Value Package
... Thanks for your insights. From what I understood in that paper, pi0 is an estimate of proportion of insignificant tests in your dataset, and that the q value is a version of FDR corrected p-values. Perhaps I am understanding this inaccurately. I agree that Bonferroni correction is the more commonly ...
written 7.1 years ago by viavialin70
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Fdr Q Values Calculations Using Q-Value Package
... Hi Everyone, I'm trying to determine the q values of my dataset using p-values generated by Fisher's tests from PLINK (allelic and genotypic). The p values are associated with SNPs relevant against clinical outcome. I am trying to determine the most significant SNPs from my analysis out of 70 SNPs ...
written 7.1 years ago by viavialin70

Latest awards to viavialin

Popular Question 2.7 years ago, created a question with more than 1,000 views. For Mapping SNPs with just position from ATG on gene
Popular Question 6.1 years ago, created a question with more than 1,000 views. For Calculating association with outcome variable and Phased Haplotypes
Popular Question 6.1 years ago, created a question with more than 1,000 views. For P Values In Plink
Popular Question 6.1 years ago, created a question with more than 1,000 views. For Tools For Predicting Functional Effects Of Snps?
Popular Question 6.1 years ago, created a question with more than 1,000 views. For Fdr Q Values Calculations Using Q-Value Package
Popular Question 6.1 years ago, created a question with more than 1,000 views. For Significance of PLINK epistasis p-values

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