User: Gavin Kelly

gravatar for Gavin Kelly
Gavin Kelly170
Reputation:
170
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Trusted
Location:
United Kingdom / London / Francis Crick Institute
Twitter:
gavinpaulkelly
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Last seen:
1 day, 4 hours ago
Joined:
2 years, 5 months ago
Email:
g*************@gmail.com

Statistician in the Bioinformatics & Biostatistics group at the Francis Crick institute

Posts by Gavin Kelly

<prev • 47 results • page 1 of 5 • next >
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Comment: C: DESeq2 model design with unequal number of time points
... If you have a specific 'shape' of time-profile you want to investigate, then maybe using time as a continuous variable would allow you to compensate for the 'missing' timepoints.  If you kept the time term linear, then you may be able to detect genes that have differential gradient (on a log-like sc ...
written 13 days ago by Gavin Kelly170
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Comment: C: strange results from differential methylation analysis using limma
... Assuming the "data_afterpreprocessed.txt" file contains beta-values of normalised samples, in the same order as the samples in the samplesheet file, I can't see anything terribly wrong with the code. Perhaps if you do an plotMD(fit2, column=4) or volcanoplot(fit2, coef=4) you might see what's drivin ...
written 15 days ago by Gavin Kelly170
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Comment: C: DESEq2 Paired samples: Baseline Versus each Timepoint
... Minor typo that might confuse a newbie: contrast=c("Timepoint", "Day1", "Baseline") ?     ...
written 15 days ago by Gavin Kelly170
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Comment: C: LIMMA paired analysis adjusting for two continuous variables - microarray data
... Don't think there's an issue with the continuous variables being constant within the subjects - does everything work ok if you have a design with of ~bmi + age + class, with a blocking factor of id?   I suppose you could add age:class (and/or bmi:class) interaction if you're worried that a gene's a ...
written 20 days ago by Gavin Kelly170
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Answer: A: LIMMA paired analysis adjusting for two continuous variables - microarray data
... I don't think is quite right  - the class:ID term means that a coefficient will be estimated for each unique {ID, class} combination, so you'll get lots of coefficients corresponding to this term (unless you've left ID as a numeric variable - you must convert it to a factor before putting it into th ...
written 20 days ago by Gavin Kelly170
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Comment: C: how to plot does response curve for temperature
... Sounds like you're mis-intepreting the advice.  Something along the lines eval(parse(text=TPP:::fctSigmoidTR(deriv=2)), list(Pl=1, a=2, b=3, x=1)) will give you an evaluation of a sigmoidal curve with the parameters that I've put in the list, at the point x=1.  You'll need to extract your fitted ...
written 23 days ago by Gavin Kelly170
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Answer: A: how to plot does response curve for temperature
... Not really sure exactly what you're trying to achieve here, but if you're insisting on using eval, then you'd need something more like y <- eval(parse(text = "TPP:::fctSigmoidTR(deriv=deriv)"), list(deriv=2, hill=hill)) the fctSigmoid function needs a deriv parameter, and doesn't necessarily e ...
written 23 days ago by Gavin Kelly170
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Answer: A: extracting the genes associated with the clusters
... I guess you mean extract the names of genes that correspond to parts of the dendrogram? It depends on which method you use to create the dendrogram.  If you've got one, such as pheatmap, that returns the hclust objects, then you can use cutree to get the labels of the genes.  So it's just a questio ...
written 23 days ago by Gavin Kelly170
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Answer: A: Issues about experiment design
... To get the overall pre vs post, taking account of the pairing, you'll need ~treat_status + object and the second coefficient will give you the log fold-change estimate of the pre vs post (it'll be relative to 'post' if you've kept the default alphabetic factor order). So topTable(..., coef=2), or to ...
written 27 days ago by Gavin Kelly170
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Answer: A: Timecourse Differential expression with multiple factors
... I think you're going to be hard-pushed to have a single contrast that directly answers the question (and that is readily understandable by any reviewers!)  A venn-diagram approach (with all its concomitant crudities of multiple exposure to statistical error, and lack of detecting different degrees o ...
written 28 days ago by Gavin Kelly170

Latest awards to Gavin Kelly

Scholar 23 days ago, created an answer that has been accepted. For A: DESeq2 3-fatcor design and different interaction terms
Teacher 23 days ago, created an answer with at least 3 up-votes. For A: extracting the genes associated with the clusters
Autobiographer 4 weeks ago, has more than 80 characters in the information field of the user's profile.
Scholar 16 months ago, created an answer that has been accepted. For A: DESeq2 3-fatcor design and different interaction terms

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