User: i.sudbery

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i.sudbery10
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Posts by i.sudbery

<prev • 16 results • page 1 of 2 • next >
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Comment: C: Extracting within subject effect in a between and within subject model with DESe
... 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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Extracting within subject effect in a between and within subject model with DESeq2
... 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: ...
deseq2 design written 16 days ago by i.sudbery10 • updated 15 days ago by Michael Love23k
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Comment: C: Batch Correction with only one sample in a batch
... 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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Batch Correction with only one sample in a batch
... 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 ...
limma deseq2 batch effect written 11 months ago by i.sudbery10 • updated 11 months ago by Ryan C. Thompson7.3k
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Meaning oflLog2fold change in DEXseqResults object
... 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 ...
dexseq written 18 months ago by i.sudbery10
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Comment: C: GOseq: Correct for gene length or read count?
... 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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GOseq: Correct for gene length or read count?
... 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 ...
goseq dexseq written 20 months ago by i.sudbery10
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Comment: C: DESeq2 and shrinkage of log2 fold changes
... 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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Comment: C: Reactome pathways in ReactomeDB/graphite
... 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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Reactome pathways in ReactomeDB/graphite
... 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, ...
graphite reactome reactomepa written 2.3 years ago by i.sudbery10 • updated 2.3 years ago by gabriele.sales100

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