User: Lemire

gravatar for Lemire
Lemire570
Reputation:
570
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Trusted
Location:
Canada
Last seen:
3 weeks ago
Joined:
4 years, 9 months ago
Email:
l*******@yahoo.ca

Posts by Lemire

<prev • 50 results • page 2 of 5 • next >
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Answer: A: GCTA tool for case-control association analysis
... I was the one suggesting GCTA in addition to GEMMA to deal with relatedness. I am not as familiar with GCTA, but GEMMA deals with case/controls as if it was a quantitative trait, using the following justification (from the manual): "For binary traits, one can label controls as 0 and cases as 1, an ...
written 3 months ago by Lemire570
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Comment: C: Log-transformation, coefficient of variation, standard error and mass-spectromet
... The problem you are facing is that the log of a mean is not the same as the mean of logs. Same for SD. But you know, it's possible that the log scale is a natural scale for your experiment, especially since you mention intensities. In which case, you could work straight from the log-transformed valu ...
written 3 months ago by Lemire570
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Answer: A: Variant association analysis with both related and unrelated individuals
... You can use GEMMA, which implements linear mixed models to correct for structures in your sample (relatedness and population stratification). https://github.com/genetics-statistics/GEMMA/blob/master/README.md In addition, I believe GCTA can do the same thing: https://cnsgenomics.com/software/gcta ...
written 3 months ago by Lemire570
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Comment: C: Missing snps in PRSice
... Could they be A/T and C/G SNPs? Those are excluded by PRSice. Without knowledge of strand, the risk allele can't be determined. ...
written 4 months ago by Lemire570
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Answer: A: logistic regression using HLA alllelic data
... Find a way to produce a data frame containing the counts of each alleles that you see, and the case-controls status. E.g. (fake data) > df DX DRB1.0401 DRB1.0404 DRB1.0405 DRB1.0408 1 0 0 0 1 1 2 0 0 0 0 2 ...
written 6 months ago by Lemire570
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Comment: C: How to make Q-Q plots for different models at a single chart using R?
... With abline( 0,1 ) ...
written 6 months ago by Lemire570
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Answer: A: How to make Q-Q plots for different models at a single chart using R?
... You could plot it outside any qq plotting functions. The following will generate the same graph: Generate p-values: p<- runif( 10000 ) Using qqplot: qqplot( -log10( ppoints(p ) ), -log10( p ) , col="red" ) Using plot: p.sorted <- sort(p) plot( -log10(ppoints(p.sorted )) ...
written 6 months ago by Lemire570
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Answer: A: GWAS in mixed populations
... Your results might possibly be spurious due to population stratification. You have allelic frequency differences between your population, and if the trait distribution also vary between your populations, then your results will likely be confounded. Unless you accounted for the different population ...
written 6 months ago by Lemire570
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Answer: A: Estimating heritability of a trait from data containing siblings
... If you meant SNP heritability calculated from methods that estimates a genetic relationship matrix (GRM, such as calculated by, e.g., GCTA), then yes, including siblings will potentially drive up the estimates (unless you account for them, which is not the default). That's because the underlying as ...
written 8 months ago by Lemire570
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Answer: A: Regression models on genetic data
... In your regression equation, you have the following terms: beta_s * SNP + beta_i * SNP * exposure (ignoring the other ones you may have) The estimate for beta_s (from which you derived your significance) is the slope of the effect of the SNP on your outcome **when the exposure variable is equal to ...
written 9 months ago by Lemire570

Latest awards to Lemire

Scholar 4 months ago, created an answer that has been accepted. For A: Detecting fine population structure such as might confound a rare variant associ
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Detecting fine population structure such as might confound a rare variant associ
Scholar 6 months ago, created an answer that has been accepted. For A: Detecting fine population structure such as might confound a rare variant associ
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Detecting fine population structure such as might confound a rare variant associ
Scholar 2.4 years ago, created an answer that has been accepted. For A: Detecting fine population structure such as might confound a rare variant associ
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Detecting fine population structure such as might confound a rare variant associ
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Non A T G C base in RefSeq zebrafish mRNA sequence
Popular Question 4.0 years ago, created a question with more than 1,000 views. For CELLULOID: tumor ploidy, cellularity, subclonal copy number events
Teacher 4.1 years ago, created an answer with at least 3 up-votes. For A: Detecting fine population structure such as might confound a rare variant associ
Teacher 4.5 years ago, created an answer with at least 3 up-votes. For A: Detecting fine population structure such as might confound a rare variant associ
Scholar 4.6 years ago, created an answer that has been accepted. For A: Detecting fine population structure such as might confound a rare variant associ
Scholar 4.7 years ago, created an answer that has been accepted. For A: Detecting fine population structure such as might confound a rare variant associ
Teacher 4.7 years ago, created an answer with at least 3 up-votes. For A: Detecting fine population structure such as might confound a rare variant associ

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