Moderator: andrew.j.skelton73

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Posts by andrew.j.skelton73

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Comment: C: Time Course RNA-Seq
... This is certainly an old post, however the approach I outlined is still valid. I'd spend some time thinking about what your experimental question is based on time. Another approach might be fit a cubic spline curve - see section 9.6.2 of the limma users guide. Mostly the *best* statistical approac ...
written 3 months ago by andrew.j.skelton736.0k
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Comment: C: Keep the paired reads whose length less than 400,000 bp
... Ah, I think you're referring to the insert size. Check out [this][1] post on filtering a bam file on insert size. Also you can use the [bbmap][2] tools to look at a histogram of your insert size for some diagnostics [1]: https://www.biostars.org/p/95822/ [2]: https://jgi.doe.gov/data-and-tools ...
written 6 months ago by andrew.j.skelton736.0k
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Answer: A: How to interpret a Stringdb interaction network of a mouse-proteomics dataset wh
... Your protein identifiers are human. Take P10809 as an example - [Uniprot Entry][1] - P10809 (CH60_HUMAN), 60 kDa heat shock protein, mitochondrial, HSPD1, Homo sapiens (Human) - [Mouse Uniprot Entry][2] - P63038 (CH60_MOUSE), 60 kDa heat shock protein, mitochondrial, Hspd1, Mus musculus (Mouse) ...
written 11 months ago by andrew.j.skelton736.0k
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Answer: A: Visualising individual humans in RNA-seq
... This is certainly a tricky problem. My favourite method for exploring what's happening with individual samples is [GSVA][1]. GSVA takes your expression matrix (genes x samples) and a set of gene sets (pathways, functions, whatever you like), and calculates a score that summarises the geneset for a g ...
written 11 months ago by andrew.j.skelton736.0k
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Comment: C: cross platform microarray normalization
... Hi, @ghataksoumyakanti - This thread is nearly 4 years old. Please open a new question with lots of detail to ensure that users can help you out! - [See here for how to ask a good question][1] [1]: https://www.biostars.org/p/75548/ ...
written 11 months ago by andrew.j.skelton736.0k
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Comment: C: Vcf produced after ApplyVSQR step
... Can you clarify if this is WES / WGS / Targeted sequencing? ...
written 14 months ago by andrew.j.skelton736.0k
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Answer: A: Vcf produced after ApplyVSQR step
... I'd check out [this post][1] which tries to explain VQSR all in one. Particularly look at the *How ApplyRecalibration works in a nutshell* section: > During the first part of the recalibration process, variants in your > callset were given a score called VQSLOD. At the same time, variants &g ...
written 15 months ago by andrew.j.skelton736.0k
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Comment: C: Vcf produced after ApplyVSQR step
... I've formatted your post so that your code blocks are more readable ...
written 15 months ago by andrew.j.skelton736.0k
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Comment: C: Investigating differentially expressed genes
... Do you have the loci of each SNP in a file? Also reference genome builds may play a role here - are they different between the RNAseq and GWAS platform? ...
written 15 months ago by andrew.j.skelton736.0k
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Answer: A: Kolmogorov-Smirnov Test and Shapiro-Wilk Test statistics in Proteomics
... This seems like you want to understand why these "geeky" mathematical principles are relevant to statistical modelling of biological data. This is beyond proteomics, but more orientated to fundamental assumptions of modelling. I'd recommend reading Wolfgang Huber & Susan Holmes' book, Modern Sta ...
written 15 months ago by andrew.j.skelton736.0k

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