User: HumeMarx

gravatar for HumeMarx
HumeMarx20
Reputation:
20
Status:
New User
Location:
United Kingdom
Last seen:
2 days, 20 hours ago
Joined:
5 years, 7 months ago
Email:
m*******@hotmail.com

Posts by HumeMarx

<prev • 30 results • page 1 of 3 • next >
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Answer: A: Why is Affymetrix computed sex different to that of plink?
... 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 HumeMarx20
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Obtaining a list of SNPs that do not vary in different populations
... 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 ...
maf hapmap plink written 4.2 years ago by HumeMarx20
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Why is Affymetrix computed sex different to that of plink?
... 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 ...
plink2 axiom analysis suite genotyping written 4.5 years ago by HumeMarx20
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Answer: A: Multivariate models with haplotypes and SNPs at the same time
... did you ever find an answer? ...
written 4.9 years ago by HumeMarx20
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Comment: C: What can be causing my very odd data?
... 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 ...
written 5.0 years ago by HumeMarx20 • updated 13 months ago by _r_am32k
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What can be causing my very odd data?
... 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 ...
exome sequencing pca plink missing genotypes written 5.1 years ago by HumeMarx20
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Comment: A: Plink-GWAS- how to solve heterozygous haploid warning in data cleaning
... 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 ...
written 5.1 years ago by HumeMarx20 • updated 13 months ago by _r_am32k
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Comment: C: Area under the ROC Curve for genetic data
... Thank you, this is most useful. Thanks ...
written 5.4 years ago by HumeMarx20
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Answer: A: Area under the ROC Curve for genetic data
... Surely someone must have an answer to this...  ...
written 5.4 years ago by HumeMarx20
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Area under the ROC Curve for genetic data
... 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 ...
latest R rocr area under the curve written 5.4 years ago by HumeMarx20 • updated 5.4 years ago by Shicheng Guo8.5k

Latest awards to HumeMarx

Popular Question 12 months ago, created a question with more than 1,000 views. For What can be causing my very odd data?
Epic Question 2.7 years ago, created a question with more than 10,000 views. For compare two files and print unique values to a new file
Popular Question 2.7 years ago, created a question with more than 1,000 views. For What can be causing my very odd data?
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Can I un index a vcf.gz.tbi file?
Popular Question 2.7 years ago, created a question with more than 1,000 views. For compare two files and print unique values to a new file
Popular Question 2.7 years ago, created a question with more than 1,000 views. For WES vcf file doesn't have any SNP IDs, only position
Great Question 3.5 years ago, created a question with more than 5,000 views. For compare two files and print unique values to a new file
Popular Question 3.5 years ago, created a question with more than 1,000 views. For compare two files and print unique values to a new file
Popular Question 4.1 years ago, created a question with more than 1,000 views. For compare two files and print unique values to a new file
Popular Question 4.9 years ago, created a question with more than 1,000 views. For compare two files and print unique values to a new file
Supporter 5.1 years ago, voted at least 25 times.

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