## User: i.sudbery

i.sudbery10
Reputation:
10
Status:
New User
Location:
European Union
Last seen:
2 weeks, 1 day ago
Joined:
3 years, 10 months ago
Email:
i********@sheffield.ac.uk

#### Posts by i.sudbery

<prev • 16 results • page 1 of 2 • next >
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... Thanks for that - I think I follow what you are saying about extracting the genotype main effect. I'm less sure about extracting the average treatment effect - wouldn't extracting this from ~genotype + treatment mean you weren't controlling for mouse specific effects (which I think are pretty larg ...
written 15 days ago by i.sudbery10
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... I am analysing an experiment where three mice of one genotype and 5 of another have been treated with a drug, and samples taken before and after treatment. This is thus a "between and within subject" design, with the design ~genotype + genotype:mouse + genotype:treatment i think. We wish to ask: ...
written 16 days ago by i.sudbery10 • updated 15 days ago by Michael Love23k
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... We don't *KNOW* that there is a significant batch effect. Indeed, we don't see any obvious evidence of one on, for example, MDS plots. However, we do know we have batches, and that batches can have effects. How would we determine if it was better to remove, say a third of our samples, or to not corr ...
written 11 months ago by i.sudbery10
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... We have an experiment where samples were collected and sequenced in several batch (matched ATACseq and RNAseq). We would like to include the batch in our analysis formula if possible. The problem is that after quality control and removing substandard samples, some of the batches have only one sample ...
written 11 months ago by i.sudbery10 • updated 11 months ago by Ryan C. Thompson7.3k
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... After completeing a DEXseq analysis with the following code: dxd <- DEXSeqDataSet(counts, col_data, design= ~ sample + exon + condition:exon, featureID = mcols(gffs)$exon_id, groupID = mcols(gffs)$gene_id, feature ...
written 18 months ago by i.sudbery10
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... Arrggh. Sorry, pasted the wrong piece of code in. Will edit. Good call on the widest range. To my eyes at least, the logistic model suggests that length and expression have at least some independent affect on P(DE), as, in fact, does there interaction. Logging the expression (+1 count) gives a nice ...
written 20 months ago by i.sudbery10
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... I am interested in whether a protein is involved in intron retention.I have used DEXSeq to call differentially used exons from two conditions, and then isolated which of those exons represent intron retention events. To test for functional enrichment I build a dataframe that contains gene_id, the l ...
written 20 months ago by i.sudbery10
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... Hi Mike, would I be right in thinking that another situation you might not want to use shrinkage is if you wanted to compare the change for two sets of genes, and one of the those sets was more lowly expressed than the other? ...
written 23 months ago by i.sudbery10
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... Thanks, that makes perfect sense! It would then seem that using graphite as input to ReactomePA is possibly inappropriate as several of the analyses relie in part on enrichment analysis or perhaps it is a bit weird that such a reaction is listed as part of the "pathway", when really it just means th ...
written 2.3 years ago by i.sudbery10
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... ReactomePA pathway plots generated using viewPathway seem to be missing components of the pathway. For example if you view the human "HDL-mediated lipid transport" using viewPathway, the resulting network has 14 nodes. However, if you get any of the pathway mapping files from the reactome website, ...
written 2.3 years ago by i.sudbery10 • updated 2.3 years ago by gabriele.sales100

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