User: Lemire

gravatar for Lemire
Lemire560
Reputation:
560
Status:
Trusted
Location:
Canada
Last seen:
1 week, 2 days ago
Joined:
4 years, 6 months ago
Email:
l*******@yahoo.ca

Posts by Lemire

<prev • 45 results • page 1 of 5 • next >
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Comment: C: What is the relationship between PLINK --pca and --mds-plot in terms of % varian
... MDS, just like PCA, has as many dimensions as there are variables. I don't know the specifics of the implementation, but my guess is if you specify 10, it will likely just give you the first 10 dimensions. This means that if you ask for 10, and then 20 in a second run, the first 10 should be the sa ...
written 11 days ago by Lemire560
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Comment: C: What is the relationship between PLINK --pca and --mds-plot in terms of % varian
... You need ALL eigenvalues, not just the first 20. The default is to output just 20, but there are actually as many eigenvalues as you have samples. Count your number of samples, and pass that as argument. In practice, at some point the eigenvalues get really small, but depending on your sample size ...
written 12 days ago by Lemire560
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Answer: A: Meta-Analysis effect size is not in the same direction as GWAS effect sizes.
... I think it's just your interpretation of the output that is incorrect, with respect to which allele the effect size is based on. Read and re-read the documentation, it can be confusing sometimes. With regards to your meta-analysis estimates, they seem correct (albeit the sign), so it's not a soft ...
written 25 days ago by Lemire560
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Comment: C: Population Genetics: Identity by State measure
... Your measures are frequency-dependent. If your sample contains individuals of mixed ancestry or admixed, your percentages would be off from what you expect. Contamination could also explain off-percentages (samples with high heterozygosity). Otherwise, if your sample is homogeneous in terms of anc ...
written 4 weeks ago by Lemire560
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Comment: C: how to fix this error: duplicate 'row.names' are not allowed read.table
... 1) you should have 3 files, yet you only pasted one 2) via="csv", yet the dataset you pasted is not comma-separated 3) skip=rep(1:3), yet from man page "skip: a vecter [sic] of size K (the number of data sets) composes [sic] of 1 or 2. see 'Details'." Just type rep(1:3) in R to see what I mean. ...
written 5 weeks ago by Lemire560
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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 6 weeks ago by Lemire560
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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 6 weeks ago by Lemire560
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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 7 weeks ago by Lemire560
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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 10 weeks ago by Lemire560
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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 4 months ago by Lemire560

Latest awards to Lemire

Scholar 10 weeks ago, created an answer that has been accepted. For A: Detecting fine population structure such as might confound a rare variant associ
Teacher 4 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 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 11 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 2.2 years ago, created an answer that has been accepted. For A: Detecting fine population structure such as might confound a rare variant associ
Teacher 2.2 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 2.2 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 3.8 years ago, created a question with more than 1,000 views. For CELLULOID: tumor ploidy, cellularity, subclonal copy number events
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
Teacher 4.4 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
Scholar 4.4 years ago, created an answer that has been accepted. For A: Detecting fine population structure such as might confound a rare variant associ
Scholar 4.6 years ago, created an answer that has been accepted. For A: Detecting fine population structure such as might confound a rare variant associ
Teacher 4.6 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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