User: Ahill

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Ahill820
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Posts by Ahill

<prev • 75 results • page 1 of 8 • next >
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Answer: A: SNPRelate data file
... Instructions to create a GDS file: http://corearray.sourceforge.net/tutorials/SNPRelate/#create-a-gds-file-of-your-own ...
written 19 days ago by Ahill820
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Comment: C: Normalisation of arrays with global changes expected
... Just speculating, but two approaches to select a control gene set would be selection of "known" housekeeping genes (e.g. GAPDH, Actin, etc.), or rank invariant set normalization to select genes whose ranks are stable across samples (original ref I believe at https://www.ncbi.nlm.nih.gov/pmc/articles ...
written 20 days ago by Ahill820
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Comment: C: Getting Risk Allele from GWAS Odds Ratio?
... Interested in responses on this. I'd think fundamentally there is no way to reliably infer risk allele given only p/odds ratio for a SNP. I think it's a common, but not certainly not universal, convention that the minor allele is used as effect allele in common software used to compute association ...
written 5 weeks ago by Ahill820
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Comment: C: Intersection of flow cytometry and bioinformatics
... In immunophenotyping, some common goals are to either quantify the number of cells in previously defined cell populations, or to identify new, previously unknown groups of cells that correlate with a response of interest. In both those cases, "bioinformatics" approaches for supervised and unsupervi ...
written 9 weeks ago by Ahill820
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Answer: A: Unsupervised subtype discovery
... I'd say there are no hard and fast rules about how many genes to include, or what algorithm to pick, it's data-dependent. If data quality is good and there are truly sub-types to be found, you could probably succeed using any one of algorithms you list. If you are looking for a case study, this pa ...
written 11 weeks ago by Ahill820
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Answer: A: Log2FC presentation expression array
... Log ratios should be presented as signed values, where negative log-ratios indicate down-regulation and positive ones represent up-regulation. If your pre-transformed values are A and B you can compute the log-ratio as log(B)-log(A) or log(B/A), both are equivalent, assuming of course your values A ...
written 3 months ago by Ahill820
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Answer: A: Principal Component Analysis using SNP data ste
... If you are an R user, the SNPRelate package provides PCA and routines that would allow you to bring in datasets like 1000G from VCF or PLINK format files: http://corearray.sourceforge.net/tutorials/SNPRelate/#principal-component-analysis-pca http://bioinformatics.oxfordjournals.org.proxy1.athensam ...
written 3 months ago by Ahill820
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Comment: C: Ambigious sex warning using PLINK
... From the message, it appears PLINK is not recognizing the sex coding in your dataset. As first check, in your input .ped file, are you coding sex in the 5th column using the PLINK standard 1=male, 2=female, 0=unknown? See [here][1]. If sex is unknown in your input dataset, you can still continue ...
written 6 months ago by Ahill820
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Comment: C: Compare genotypes from sequencing (vcf) and microarrays (ped)
... You could use plink --vcf --recode to convert .vcf to .ped/.map (see [here][1]), and then compare .peds. Obviously this assumes variants are identified the same way your input .vcf and .ped files. Imagine you would want to filter to variants that are present in both your input sets, which could be ...
written 6 months ago by Ahill820
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Comment: C: Good repository for uploading SNP data (from genotyping array) alongside manuscr
... Have you looked at GEO? They apparently support SNP array submissions (e.g. the Affy SNP 6.0 [array][1]). Recommendations for human subject data [here][2]. Not sure they would accept PLINK binary filesets as-is, but their standard formats would not be too difficult to generate starting from PLINK ...
written 6 months ago by Ahill820

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