Moderator: andrew.j.skelton73

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Posts by andrew.j.skelton73

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Comment: C: Comparing different transcripts expression level of a list of genes from one con
... DEXseq is most likely what you want. For a single gene, you can look at the sample-wise usage metrics, such as [this visualisation][1] (third figure down). They've analysed this with a control and knockout, but you can easily just provide an intercept of 1 design (`~1`) where required. [1]: ht ...
written 11 days ago by andrew.j.skelton735.8k
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Answer: A: Comparing different transcripts expression level of a list of genes from one con
... This F1000 Article shows how to perform DTU analysis using Salmon quantification - [Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification][1] This makes use of classic packages such as DEXSeq, but optimised to use alignment-free quantifications. ...
written 11 days ago by andrew.j.skelton735.8k
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Comment: C: Divide isoform expression by gene expression to calculate splicing ratios
... This reads as you want someone to write the code for you... what have you tried? ...
written 13 days ago by andrew.j.skelton735.8k
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Answer: A: GATK -Xmx4G and -Xmx8G
... These aren't GATK specific switches, but a java JVM (java virtual machine) parameter. Since GATK4, these parameters have been absorbed into the main binary to integrate well with the WDL notation and Cromwell orchestration. `-Xmx` is the switch to tell Java how much memory it's allowed to work wit ...
written 18 days ago by andrew.j.skelton735.8k
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Answer: A: E: Package 'libbamtools-dev' has no installation candidate
... @Bastien definitely helps solve your compile dependency, but unless you've got a specific reason for compiling try out these resources which make it far easier to get bioinformatics software up and running! - [Bioconda][1] - This is the best way to run on a local system, and manage lots of dif ...
written 24 days ago by andrew.j.skelton735.8k
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Comment: C: How to run removeBatchEffect function?
... yep, that's correct. ...
written 4 weeks ago by andrew.j.skelton735.8k
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Answer: A: How to run removeBatchEffect function?
... You don't want the fit being passed to the function, you want something that can be processed by the `getEAWP` function - such as the `voom` object (`v` in your case). `getEAWP` will get the right information from your `voom` object, but it's expecting an expression matrix as input. Check out the pa ...
written 4 weeks ago by andrew.j.skelton735.8k
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Comment: C: EnhancedVulcano Package Inputing Data Format
... look at `colnames(VE_data)` to make sure that excel hasn't added any whitespace. ...
written 8 weeks ago by andrew.j.skelton735.8k
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Comment: C: Infinium Methylation SNP
... Minor Allele Frequency (MAF) - Measured differences in methylation could actually be a source of genetic variation in your population, thus if you want to minimise that bias then this function removes those probes. ...
written 10 weeks ago by andrew.j.skelton735.8k
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Comment: C: DNA methylation analysis with RnBeads: start analysis from Beta-values
... This answer is three years old, and I'm struggling to see the point of this comment other than a plug for your package? The point of using M values is that Limma fits a homoskedastic model, and M values are homoskedastic. Beta values are heteroskedastic mostly in the <0.2 & >0.8 regions [1 ...
written 11 weeks ago by andrew.j.skelton735.8k

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