User: i.sudbery

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i.sudbery0
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Posts by i.sudbery

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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 15 days ago by i.sudbery0
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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 4 months ago by i.sudbery0
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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 4 months ago by i.sudbery0 • updated 4 months ago by gabriele.sales70
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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 5 months ago by i.sudbery0 • updated 5 months ago by Aaron Lun14k
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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 23 months ago by i.sudbery0
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Comment: C: Resummarisation of Exon array normalised at probeset level to gene level
... Do you think if I took the mean of probes for each gene, that the resulting values would be valid for downstream limma analysis? ...
written 23 months ago by i.sudbery0
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Resummarisation of Exon array normalised at probeset level to gene level
... We wish to analyse an Exon Array dataset we obtained from a public source (unfortunately not GEO). The data we have is a matrix of RMA normalised expression values from some 400 Exon arrays summarized at the probeset level. We are only interested in the gene level and wondered if there is any way to ...
normalization limma oligo written 23 months ago by i.sudbery0 • updated 23 months ago by James W. MacDonald43k
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Comment: C: DEXSeq: Testing only a subset of exons
... Hi Alejandro, Depends what you mean by change. The dispersions are slightly higher in the retained intron only analysis (best fit about 1.1 fold higher). However, everything that was significant doing the complete analysis is also significant in the subsetted analysis and then some more. My problem ...
written 23 months ago by i.sudbery0
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DEXSeq: Testing only a subset of exons
... In DEXSeq is it possible (advisable) to test only a subset of exons for differential usage? I am currently working on a project where we are only interested in retained intron usage. Being able to test for only a subset of events would a) increase power b) reduce compute time (currently about 16hrs ...
dexseq written 23 months ago by i.sudbery0

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