User: andrew.j.skelton73

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Posts by andrew.j.skelton73

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Answer: A: Alternatives to Venn Diagrams
... I can't recommend [UpsetR][1] enough as an alternative to Venn diagrams, for pretty much any set based visualisation. It's available in CRAN and very efficient. If OncoPrint fit's your use case better (which it sounds like might), then I'd take @Kevin's answer. [1]: https://github.com/hms-dbmi/ ...
written 7 days ago by andrew.j.skelton734.1k
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Comment: C: User Friendly VCF Filtering Tools
... I'd consider annotation tools to be a separate issue, while tools such as VEP can produce tab delimited output, the crux of this post is then how to present / filter these annotations in a user friendly way. ...
written 18 days ago by andrew.j.skelton734.1k
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Answer: A: Bayesian Estimation of Temporal Regulation-RNASeq
... When looking at a whole time course, you can look at the [timecourse][1] package which implements the Hotelling T2 test. Alternatively, you could use packages such as [Limma][2] to look for non-linear trends via splines using functions such as [ns][3] (natural cubic spline). I did something similar ...
written 21 days ago by andrew.j.skelton734.1k
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Comment: C: how to automate microarray data analysis
... Check out the [Limma][1] package [1]: https://bioconductor.org/packages/release/bioc/html/limma.html ...
written 23 days ago by andrew.j.skelton734.1k
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Comment: C: Error when run testForDEU DEXSeq
... Check `str(dsd)` after calling `DEXSeqDataSetFromHTSeq `, and again when subsetting. I suspect you've somehow made that object into a list rather than a DESeq2 object. ...
written 24 days ago by andrew.j.skelton734.1k
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Answer: A: probe's p.value in 450 k array
... I'm assuming that you're referencing detection P values, which represent the confidence that the scanner detected what it's reporting. These are internally determined within the scanner (as far as I know). These p values are useful to remove spurious observations that are close to background, as the ...
written 24 days ago by andrew.j.skelton734.1k
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Answer: A: How to convert VCF file into a binary matrix to find the genotype markers
... I'm assuming here that you're looking for Plink format. You'll need to download the 1KG vcf file for the populations you're interested in, and then run something like: ./vcftools --vcf ./1KG.vcf --plink-tped --out plinkformat ...
written 25 days ago by andrew.j.skelton734.1k
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Comment: C: Read count correlation between samples
... Very comprehensive response for such a vague question! +1 ...
written 28 days ago by andrew.j.skelton734.1k
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Comment: C: Infinium Methylation SNP
... The capture sequence is the genomic sequence that encapsulated the CpG site, and attaches to the oligonucleotide bead on the array. ...
written 29 days ago by andrew.j.skelton734.1k
0
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Answer: A: Infinium Methylation SNP
... If you're using Minfi (and by extension `IlluminaHumanMethylation450kanno.ilmn12.hg19`), there's 3 types of position that can be filtered with the `dropLociWithSnps` function, leveraging the `snps` parameter: `SBE`, `CpG`, and `Probe`. SBE is the single base extension, CpG is the actual CpG capture ...
written 29 days ago by andrew.j.skelton734.1k

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