User: seta

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seta1.4k
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Posts by seta

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The same effect of SNPs in LD?
... Dear friends, Regarding the association analysis for a given trait, could you please clear me if there is a similar effect size or at least an effect in the same direction for SNPs in linkage disequilibrium? Thanks ...
gwas linkage disequilibrium effect size written 5 weeks ago by seta1.4k
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PLINK beta coefficient
... Dear all, I analyze the genetic variation association with a given quantitative trait using PLINK. As I found, this tool reported a beta coefficient per one minor risk allele; so, this value (beta) will be multiplied in 2 for the individuals with two minor risk alleles, yes? However, the beta value ...
gwas association plink beta coefficient written 8 weeks ago by seta1.4k
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Comment: C: PLINK basic command line usage
... Please just use HapMap_3_r3_1 for the file name. Also, it is required to add "--mind N" and "--geno N" after the --missing flag to check missingness per individual and Missingness per marker, respectively. The individuals or marker will be removed based on the missing rate threshold that you can d ...
written 3 months ago by seta1.4k
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Comment: C: WGCNA soft-threshold power selection
... Hi Kevin, Although it's late, thank you for your feedback. You mentioned that the dataset is possibly flatted? did you say due to the negative signed R2? please kindly tell me how to solve this issue? ...
written 3 months ago by seta1.4k
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Comment: C: GWAS results and linkage disequilibrium issue
... Thanks for your comment; could you please let me know how successful is finding the causal SNP for complex diseases? Regarding risk score calculation, however, the other risk SNPs (not necessarily causal, but associated or in high LD) existed and have their own effects, so why we don't consider the ...
written 3 months ago by seta1.4k
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GWAS results and linkage disequilibrium issue
... Dear all, Regarding the GWAS results, assuming there are 10 significant associated SNPs with a given trait that are in high LD. If all significant associated SNPs should be reported or just those are not in LD? I saw both in the various papers, what's your idea about it? Also, regarding the risk ...
gwas linkage disequilibrium ld risk score written 3 months ago by seta1.4k
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Comment: C: real time pcr primer design
... You can design the primers from the conserved region of different isoforms if you have no idea which isoform is expressed in your experiment. ...
written 3 months ago by seta1.4k
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Comment: C: edgeR normalization via TMM method
... Thank you for the great video. However, I have some questions, hope to find the answer. In the video, he says “edgeR filters out the biased genes based on their log differences”, then he calculates the log2 (reference, gene 1/ sample 2, gene1). Here, I got confused about 1) why the ratio calculated ...
written 3 months ago by seta1.4k
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edgeR normalization via TMM method
... Dear all, Could you please clear me how edgeR solve the compositional bias within an RNA-seq library via TMM method? if it removes the highly expressed genes or if it allocates lower weight (via the normalization factor of less than 1) to them? Thanks ...
rna-seq edger normalization tmm written 3 months ago by seta1.4k • updated 3 months ago by ATpoint44k
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Comment: C: Why 'filterByExpr' does not eliminate low read counts from the expression data?
... Dear all, As far as I know, CPM threshold 0.5 (corresponded to 10 counts) is recommended for a 20 million reads library, isn't it? Could you kindly clear me which CPM threshold will be used for filtering by `filterByExpr` function? ...
written 3 months ago by seta1.4k

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