User: whtopjazz

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whtopjazz0
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Posts by whtopjazz

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Difference between EWAS and differential methylation analysis? (similar for TWAS and differential expression analysis)
... Difference between EWAS and differential methylation analysis? (similar for TWAS and differential expression analysis). I thought they are the same thing ...
R rna-seq written 21 months ago by whtopjazz0
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Should zero expression values be remove in eQTL analysis?
... For example, RNA-seq expression for gene1 in 10 people are, GENE1=[0, 0, 1, 2, 3, 4, 3, 4, 2, 7]。 SNP1 with alleles A and G, and SNP1 in 10 people is SNP1=[0, 1, 2, 1, 1, 2, 2, 2, 0, 0], 0 means GG, 1 means AG, 2 means AA。 What I want to do it eQTL analysis. Simple put, I want to fit a linear mode ...
rna-seq snp written 2.2 years ago by whtopjazz0 • updated 2.2 years ago by Fabio Marroni2.7k
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LD pruning before imputation?
... I'm new to imputation. And I filtered samples and markers before imputation. But I do not know, if I should filter SNPs by LD before imputation. For example, use plink `--indep-pairwise 50 1 0.75` to remove SNPs in high LD. Can anyone explain why should I do that or not? Thanks ...
snp impute plink ld written 2.3 years ago by whtopjazz0 • updated 2.3 years ago by zx87549.9k

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