User: Lemire

gravatar for Lemire
Lemire410
Reputation:
410
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Trusted
Location:
Canada
Last seen:
1 week, 5 days ago
Joined:
4 years, 1 month ago
Email:
l*******@yahoo.ca

Posts by Lemire

<prev • 32 results • page 1 of 4 • next >
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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 12 days ago by Lemire410
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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 7 weeks ago by Lemire410
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Answer: A: Infinium MethylationEPIC BeadChip probes with cross-hybridisation potential
... Check this paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4909830/ ...
written 6 months ago by Lemire410
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Answer: A: Is okay to apply ANOVA to Log2 transformed data ?
... If you are concerned about the underlying parametric assumptions, you could try Kruskal-Wallis, the non-parametric version of the ANOVA. It's rank-based, meaning you can apply it to the non-transformed data. ...
written 3.0 years ago by Lemire410
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Answer: A: Whole exome sequencing data, rare variants and QQ-plots
... QC has likely nothing to do with your problem. Here are two things you need to think about: 1. you're using a 2df test (genotypic?) for rare variants even though some of your cell counts are likely to be 0. 2. You're using a qq-plot designed to assess the distribution of a continuous variable when ...
written 3.4 years ago by Lemire410 • updated 12 months ago by zx87548.2k
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Answer: A: Bioinformatics analyses hall of shame
... Just go to https://pubpeer.com/ ...
written 3.4 years ago by Lemire410
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Answer: A: How to Assess Paired Sample Data from WES
... This is an answer to the question you actually asked: Look up http://genome.sph.umich.edu/wiki/VerifyBamID ...
written 3.4 years ago by Lemire410
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Answer: A: Why are there too many mutations in controls, but not in tumour?
... That's probably loss of heterozygosity, not somatic substitutions. Caused by chromosomal regions where one parental copy was loss in the tumor (i.e. deleted). Check if they tend to cluster in regions. ...
written 3.5 years ago by Lemire410
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Answer: A: IGV not showing the variants detected by GATK and Varscan
... Try playing with the viewing options under the "Alignment" tab under Preferences (or similar for your OS).  In particular, uncheck the "Downsample reads" box.   ...
written 3.9 years ago by Lemire410
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Answer: A: LOD score of a single genotype
... It's been over 10 years I dealt with linkage, but let me have a try... To illustrate, I downloaded the test examples (datafile.dat and pedfile.dat) at http://bioinfo.cs.technion.ac.il/superlink/ I modified the last two line of datafile.dat: 0.0000 << RECOMBINATION VALUES 1 0.0500 0.50000 &l ...
written 3.9 years ago by Lemire410

Latest awards to Lemire

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 21 months ago, created an answer that has been accepted. For A: Detecting fine population structure such as might confound a rare variant associ
Teacher 21 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
Teacher 21 months 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 3.4 years ago, created a question with more than 1,000 views. For CELLULOID: tumor ploidy, cellularity, subclonal copy number events
Teacher 3.4 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 3.9 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 4.0 years ago, created an answer that has been accepted. For A: Detecting fine population structure such as might confound a rare variant associ
Scholar 4.1 years ago, created an answer that has been accepted. For A: Detecting fine population structure such as might confound a rare variant associ
Teacher 4.1 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

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