User: Kevin R. Coombes

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Posts by Kevin R. Coombes

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Comment: C: Which application to start BioConductor?
... Hi, Because BioConductor is so large, it can be hard for new investigators (or older investigators who haven't used it regularly) to figure out where to start . To help address this issue, we have developed an experimental tool that provides an interactive graphical overview of BioConductor. The ...
written 9.7 years ago by Kevin R. Coombes70
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Comment: C: MedlineR
... A couple of suggestions. First, instead of performing a single "OR" search, perform two separate searches. The "AND" search is then really easy to compute by looking at how many PMID's show up in both the searches. (This may not matter a lot with just two categories, but it will be much more effici ...
written 10.9 years ago by Kevin R. Coombes70
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Comment: C: MedlineR
... I suspect that the email address in your message will not work, since Simon Lin has since moved from Duke to Northwestern. With the help of google, you can get his current email address: s-lin2 AT northwestern.edu I have no idea if he is still supporting this R package. Best, Kevi ...
written 11.0 years ago by Kevin R. Coombes70
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Comment: C: Understanding limma, fdr and topTable
... James MacDonald wrote: > > > aaron.j.mackey at gsk.com wrote: >>> I would add that removing those genes that are unchanged in any >>> sample will also help reduce the multiplicity problem. Regardless of >>> the expression level, those genes that never change exp ...
written 11.2 years ago by Kevin R. Coombes70
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Comment: C: Finding genes with significant linear regression or trend
... As Sean said, depending on how many time points you have, a linear response may not be the best model. In fact, it is unclear that any parametric model will work across all the genes in the data set. Typically, you tend to be interested in genes that "increase over time" or "decrease over time", wi ...
written 11.3 years ago by Kevin R. Coombes70
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Answer: A: DAT to CEL
... If you go to our course web site: http://bioinformatics.mdanderson.org/MicroarrayCourse/Lectures07/ and check out Lecture 1, there is a description of how DAT files are turned into CEL files. Kevin BURCIN BEKTAS wrote: > > Greetings, > > Does anybody know how affymetrix GCO ...
written 11.7 years ago by Kevin R. Coombes70
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Comment: C: understanding GOstats p-value
... All this is certainly true. However, it is not clear that the dependence makes any real qualitative difference in the results you get. See, for example Gold et al, "Enrichment analysis in high-throughput genomics - accounting for dependency in the NULL", Brief Bioinform 2007; 8:71-77 where we e ...
written 11.7 years ago by Kevin R. Coombes70

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