User: i.sudbery

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i.sudbery10
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European Union
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6 months, 1 week ago
Joined:
3 years, 5 months ago
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i********@sheffield.ac.uk

Posts by i.sudbery

<prev • 14 results • page 1 of 2 • next >
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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 7 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 7 months ago by i.sudbery10 • updated 7 months ago by Ryan C. Thompson7.1k
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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 14 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 16 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 16 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 19 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 23 months 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 23 months ago by i.sudbery10 • updated 23 months ago by gabriele.sales100
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voom on normalised counts
... Hi, We wish to do exon analysis on an existing RNA-seq dataset - we actually only need to do it for one gene. However, the only publicly accessible data is pre-normalised using a quantile normalisation. I know that this data would be unsuitable for DEXSeq (or DESeq/edgeR), but would it be valid to ...
rnaseq limma voom written 2.0 years ago by i.sudbery10 • updated 2.0 years ago by Aaron Lun21k
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Comment: C: Resummarisation of Exon array normalised at probeset level to gene level
... I'm going to ask. But the data comes from a massive consortium, and has been around for some time without being uploaded to GEO or similar, or even published. They have lots of data sets I'd like to get my hands on, but only make summarized versions of all of them availible, which is annoying becaus ...
written 3.5 years ago by i.sudbery10

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