Moderator: i.sudbery

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i.sudbery10k
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Sheffield, UK
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IanSudbery
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49 minutes ago
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5 years, 10 months ago
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i********@sheffield.ac.uk

I am a Lecturer in Bioinformatics at the University of Sheffield, where my group studies all things gene regulation, but with a particular emphasis on post-transcriptional gene regulation and RNA-processing. I am also an author of the UMI-tools, iCLIPlib, CGAT and CGAT-core packages.

Posts by i.sudbery

<prev • 892 results • page 1 of 90 • next >
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Answer: A: DESeq2 and NA adj.pvalue
... There are several stages at which an NA might be included in the adj.pvalues column in DESeq2 output. The two most likely are low expression filtering and outlier exclusion. 1. *Independent hypothesis filtering*: DESeq2 automatically finds the base expression level at which to filter in order m ...
written 49 minutes ago by i.sudbery10k
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Answer: A: ATAC-seq annotation to gene names
... There are a couple of ways you can do this. None of them are perfect. The three most obvious choices are: * Pair peak with nearest gene * Pair peak with all genes within a certain distance * Pair peak with genes where accessibility correlates with expression. For the first two, you might conside ...
written 14 hours ago by i.sudbery10k
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Comment: C: What does p-value mean ? What and how can i interpret the results
... The random chance *if the null is true* ...
written 18 hours ago by i.sudbery10k
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Comment: C: experimental design in RNA-seq differential expression analysis
... Okay. So what I'm trying to say is, the background distribution will be the same whether you leave them in or not, because even if you leave them in the enrichment tool will automatically subtract them from the number of detected genes in the experiment (as well as the number of DE genes). ...
written 19 hours ago by i.sudbery10k
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Comment: C: Does read length of RNA seq affects the results ?
... I concur. When group is 100% confounded it is mathematically impossible to correct it, irrespective of how fancy the tool you use is. ...
written 19 hours ago by i.sudbery10k
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Comment: C: What does p-value mean ? What and how can i interpret the results
... I don't agree with this, because while a low p-value makes it unlikely that a difference is due to chance, a high p-value does not make it likely that a difference is due to chance, it just means we have insufficient evidence to say anything either way. ...
written 20 hours ago by i.sudbery10k
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Answer: A: What does p-value mean ? What and how can i interpret the results
... The p-value is the probability (hence "p"-value) of the obtaining this data or more extreme data assuming the null hypothesis is true. (definition of "more extreme" is dependent on the null and alternative hypotheses) ...
written 1 day ago by i.sudbery10k
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Comment: C: Does read length of RNA seq affects the results ?
... The OP states that the read length is entirely confounded with biological condition. Thus, you won't be able to see this as a batch effect on a PCA. ...
written 1 day ago by i.sudbery10k
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Comment: C: experimental design in RNA-seq differential expression analysis
... Sorry if I'm being dense, but I'm confused. The fisher's test in enrichment analysis tags/tag counts/tag distributions arn't used, only the number of genes that are DE and the number of genes that are not DE, there is not reference distribution. ...
written 1 day ago by i.sudbery10k
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Comment: C: experimental design in RNA-seq differential expression analysis
... It would make no difference for the enrichment analysis because enrichment tools will filter the background automatically before they start. ...
written 2 days ago by i.sudbery10k

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