User: gabriel.rosser

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Posts by gabriel.rosser

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Answer: A: Single Sample GSEA (ssGSEA) and dynamic range of expression
... Returning to this old question because, IMO, it's still relevant! This is a very interesting point and example. I wonder if the reason ssGSEA works well (without the additional normalisation discussed in other comments) is that in reality there are a very large number of genes that won't have large ...
written 5 months ago by gabriel.rosser20
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Comment: C: Single Sample GSEA (ssGSEA) and dynamic range of expression
... GSEA requires two phenotypes to be specified (e.g. healthy vs disease). That isn't necessarily the case in this example - the OP may be interested in relative enrichment of a given signature across a patient cohort, for example. I think the suggestion that there are control and case samples is purel ...
written 5 months ago by gabriel.rosser20
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DMRforPairs statistical testing framework is invalid for >2 samples?
... When >2 samples are analysed using the DMRforPairs parent function, the Kruskal-Wallis test is first applied and, if p<0.05, the Mann-Whitney test is applied pairwise. Whilst this provides a guideline for which samples differ, it isn't strictly valid according to these forum discussions: Are p ...
dmrforpairs written 2.4 years ago by gabriel.rosser20
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Comment: C: How did the edgeR authors compute Figure 2 (genewise deviance statistics?)
... This is a tremendously helpful set of comments, many thanks Gordon. I take your caveat on board - the primary motivation for repeating the gof() analysis is to show my colleagues the effect of tagwise estimation. The secondary motivation is to check my own understanding, which has been vastly improv ...
written 2.5 years ago by gabriel.rosser20
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Comment: C: Question: How did the edgeR authors compute Figure 2 (genewise deviance statisti
... Thank you! That's extremely helpful. So we're actually testing how well our deviances fit the chi squared distribution (via a normal transform). Am I thinking along the right lines when I say that this is like testing the residuals for correlation in a (general) linear model? In the sense that we ar ...
written 2.5 years ago by gabriel.rosser20
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Comment: C: About experimental design of RNA-seq
... Did you send these samples for sequencing in one batch? If so, it seems unlikely that they would be prepared at different times. How 'distinct' are the expression patterns? Even a simple R^2 value might help quantify it. It sounds to me like the variation between A0, B0 and C0 that you're observin ...
written 2.5 years ago by gabriel.rosser20
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How did the edgeR authors compute Figure 2 (genewise deviance statistics?)
... I originally asked this question on Biostars and a responder suggested I try here. To avoid any duplication of effort, I will copy or link any answer. If you have a better suggestion, please let me know. Below is a copy-pasted version of my question: McCarthy, D.J., Chen, Y., and Smyth, G.K. (2012 ...
rnaseq edger differential gene expression written 2.5 years ago by gabriel.rosser20 • updated 2.5 years ago by Gordon Smyth38k

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