User: christopher medway

Reputation:
370
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Trusted
Location:
Cardiff, UK
Last seen:
1 day, 7 hours ago
Joined:
2 years, 7 months ago
Email:
c****************@gmail.com

Posts by christopher medway

<prev • 61 results • page 1 of 7 • next >
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Comment: C: Sorting the haplotypes by similarities of SNPs in R
... This will order the dataframe by "Main" and "-1" (minus1). You probably should not use numbers as headers. dat[order(dat$Main,dat$minus1),] where dat is your full data frame ...
written 5 days ago by christopher medway370
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Answer: A: Parsing Coding Seq w grep
... I assume you want to extract sequence from the GenBank file. If this is true, there are dedicated libraries that will make this a whole lot easier, See [this post][1] [1]: https://www.biostars.org/p/179518/ ...
written 15 days ago by christopher medway370
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Comment: C: mapping between gene symbol and entrez ID
... Yes I think you should be using "SYMBOL" instead of "ALIAS" ...
written 16 days ago by christopher medway370
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Answer: A: Ploting the reads overlap Gene
... Take a look at the [Gviz][1] package in R. This may be of use. [1]: https://bioconductor.org/packages/release/bioc/html/Gviz.html ...
written 19 days ago by christopher medway370
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Answer: A: Loading PLINK files to Haploview
... Open as "Linkage Format" - .ped file goes into the 'Data File' field; .info into 'Locus Information File.' ...
written 22 days ago by christopher medway370
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Comment: C: Ranking of genes in multiple samples
... I sound like you are assuming that those genes which show, on average, the highest expression across your samples will be the interesting (disease relevant) ones. I'm not sure I agree with this. Simply taking an average value will not account for the variability between samples. ...
written 23 days ago by christopher medway370
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Comment: C: Ranking of genes in multiple samples
... how many samples is 'multiple' samples? What are you ultimately trying to achieve by ranking them - what is the biological question? ...
written 23 days ago by christopher medway370
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Comment: C: gTEX normalize counts by genotype
... What do you plan to do with the normalized data? The notion of "correcting" an analysis for the effect of a specific genotype is not uncommon, and this can be done by adding it as a covariate in your regression model. I'm sure it is technically possible to do this correction / "normalization" upfron ...
written 11 weeks ago by christopher medway370
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Answer: A: Gene synonyms/aliases - Is there a way to collect them programmatically
... This [post][1] may be of use to you [1]: https://www.biostars.org/p/126277/ ...
written 3 months ago by christopher medway370
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Answer: A: p-value and FDR
... Your Bonferroni corrected threshold for n=15000 will be; 0.05/15000 = 3.33e-06. While it is reasonable to reduce the multiple testing burden by selecting a subset of genes, this should have been decided upfront (not ad-hoc). Otherwise it becomes a fishing exercise. You may want to consider doing a f ...
written 4 months ago by christopher medway370

Latest awards to christopher medway

Popular Question 3 days ago, created a question with more than 1,000 views. For Haploview error using command line ""Thread-0" java.lang.NullPointerException"
Scholar 22 days ago, created an answer that has been accepted. For C: merging plink files
Scholar 10 months ago, created an answer that has been accepted. For C: merging plink files
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Is there a quick method to extract regularly-spaced features/SNPs from a VCF fil
Scholar 13 months ago, created an answer that has been accepted. For C: merging plink files
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Is there a quick method to extract regularly-spaced features/SNPs from a VCF fil
Scholar 13 months ago, created an answer that has been accepted. For C: merging plink files

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