Moderator: andrew.j.skelton73

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Posts by andrew.j.skelton73

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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 3 months ago by andrew.j.skelton735.9k
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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 3 months ago by andrew.j.skelton735.9k
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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 3 months ago by andrew.j.skelton735.9k
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Comment: C: Vcf produced after ApplyVSQR step
... Can you clarify if this is WES / WGS / Targeted sequencing? ...
written 6 months ago by andrew.j.skelton735.9k
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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 6 months ago by andrew.j.skelton735.9k
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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 6 months ago by andrew.j.skelton735.9k
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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 6 months ago by andrew.j.skelton735.9k
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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 7 months ago by andrew.j.skelton735.9k
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Answer: A: How to obtain multiple sequence alignments of genomes of selected vertebrate spe
... Have you considered trying out Ensembl for this problem? Buffalo (or Bison), are available in the [MSA functionalities in Ensembl][1]. Here's a [video][2] on how to perform MSA of specific species using Ensembl tools. [1]: https://www.ensembl.org/info/genome/compara/multiple_genome_alignments.ht ...
written 7 months ago by andrew.j.skelton735.9k
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Answer: A: Deal with the time-course RNA-Seq datasets
... If all you're interested in (or have to work with), is the differences between time points, then that's all you can test in your experiment. [Section 9.6.1 of the Limma users guide][1] is a good basis to start from. These principles can be applied to DESeq2 too. There are other ways to look at your ...
written 7 months ago by andrew.j.skelton735.9k

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Scholar 16 months ago, created an answer that has been accepted. For A: Surrogate Variable Analysis for Complex Experimental Design
Great Question 16 months ago, created a question with more than 5,000 views. For Illumina Instrument Type from fastq?
Good Answer 17 months ago, created an answer that was upvoted at least 5 times. For A: Find SNPs in the exome from WGS data
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