User: HumeMarx
HumeMarx • 20
- Reputation:
- 20
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- New User
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- United Kingdom
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- 2 days, 20 hours ago
- Joined:
- 5 years, 7 months ago
- Email:
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Posts by HumeMarx
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... In case anyone is having massive gender inconsistencies in Plink after exporting data from Axiom Analysis Suite: This was because there was an issue in converting the Affy files to PED/MAP format using the Axiom Analysis Suite. Regenerating the files using an upgraded (bug fixed) APT solves the issu ...
written 3.6 years ago by
HumeMarx • 20
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... Hi
I am looking at some genotyped data from a custom built array, and I wanted to look at snps that have relatively the same minor allele frequencies in different populations.
How should I go about this? Is it simply a case of downloading 1000 genome data from somewhere and looking at the MAF fo ...
written 4.2 years ago by
HumeMarx • 20
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... Hi
I was wondering if someone can help me interpret the --check-sex results I am getting in plink.
When running this command (./plink --bfile file --check-sex 0.35 0.65 ycount out X) , I seem to get a lot of Problems being detected. I have done this a couple of times and ended up focusing on com ...
written 4.5 years ago by
HumeMarx • 20
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... did you ever find an answer?
...
written 4.9 years ago by
HumeMarx • 20
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... Hi
Yes the data is awful. Exactly, I have females with Y markers. That suggests a genotyping issue to me, am I right?!
Overall there are two males in the pedigree file that actually appear to be female based on the SNP data. Quite a few others that are female but have Y markers present!
By increa ...
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... Hi all
I am having a lot of difficulty with a set of case/control exome data (using Plink2 as my main analysis tool).
I have a lot of heterozygous haploid genotypes and nonmale nonmissing Y chromosome markers. A large proportion of the samples appear not to be Caucasian from pca analysis, even t ...
written 5.1 years ago by
HumeMarx • 20
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... Hi
This post was quite useful, thank you. What happens if you have done all that, but still there remains a large number of het haploid genotypes?
I have quite a few heterozygote haploid genotypes. I have removed individuals who failed sex checks, made a new chromosome code for the SNPs in the pse ...
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... Thank you, this is most useful. Thanks
...
written 5.4 years ago by
HumeMarx • 20
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... Surely someone must have an answer to this...
...
written 5.4 years ago by
HumeMarx • 20
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... Hi Biostar.
I have performed logistic regression on 3 independent sets of case/control cohorts. I now have the task of figuring out how well a collection of the SNPs implicated in the study predict disease/control status of the individual.
The package I am trying to use in R is ROCR however I can ...
written 5.4 years ago by
HumeMarx • 20
• updated
5.4 years ago by
Shicheng Guo • 8.5k
Latest awards to HumeMarx
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2.7 years ago,
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For What can be causing my very odd data?
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For Can I un index a vcf.gz.tbi file?
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For WES vcf file doesn't have any SNP IDs, only position
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For compare two files and print unique values to a new file
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