User: Jacob Michaelson

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Posts by Jacob Michaelson

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Answer: A: Rmpi loading error --- updates
... You'll have more luck posting to the r-help list since this is not a BioC-specific problem. --Jake On Fri, 2006-06-09 at 14:27 -0400, Ye, Bin wrote: > Hi, > > I've add the libmpi.so.0 path to $LD_LIBRARY_PATH, now error is: > > library("Rmpi") > Error in dyn.load(x, as.logical(lo ...
written 13.4 years ago by Jacob Michaelson320
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Comment: C: help with large Rgraphviz output
... On Tue, 2006-06-06 at 14:00 -0700, Seth Falcon wrote: > "Kimpel, Mark William" writes: > > > Seth, > > > > I am a novice at manipulating options in R and working with output > > devices. > > > > Assuming I want to set my postscript paper size as Width= 15" ...
written 13.4 years ago by Jacob Michaelson320
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yeast2 LOCUSID environment
... Hi all, I was just wondering why there is no "LOCUSID" environment associated with the yeast2 annotation package. I know from looking up some S. cerevisiae genes by hand on the Entrez Gene website that yeast genes do have the Entrez accession numbers. The lack of this environment for the yeast2 p ...
annotation yeast yeast2 written 13.4 years ago by Jacob Michaelson320 • updated 13.4 years ago by John Zhang2.9k
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Comment: C: Bayesian networks in BioC
... On May 27, 2006, at 8:08 AM, alex lam ((RI)) wrote: > > There is a package called "deal" in CRAN for Bayesian Network > Learning. Never used it before though. > > Cheers, > Alex On May 27, 2006, at 10:09 AM, Henrik Bengtsson wrote: > Another word for Bayesian networks is grap ...
written 13.4 years ago by Jacob Michaelson320
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Bayesian networks in BioC
... Hi all, I looked around on the BioC site for information on any implementations of Bayesian networks in Bioconductor. I couldn't find anything. From the literature it looks like Bayesian networks for gene expression has been around for almost as long as microarrays, yet no implementations exist i ...
bayesian written 13.4 years ago by Jacob Michaelson320 • updated 13.4 years ago by Henrik Bengtsson2.4k
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Answer: A: limma 3-way interaction
... Okay I think I get it now. I couldn't figure out what the "assign" part was for. It refers to the term in the expanded formula which led to the term(s) you're interested in, for example: a*b -> Y = int + a + b + ab 0 1 2 3 hence the line cont.ia <- diag(p)[,attr(X,"assi ...
written 13.4 years ago by Jacob Michaelson320
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limma 3-way interaction
... Hi all, A while back I found some great code on the list to test for a two-way interaction in limma: > If you only want F-tests for interactions, the following code would work: > > X <- model.matrix(~a*b) > fit <- lmFit(eset, X) > p <- ncol(X) > cont.ia <- diag(p)[,at ...
safe written 13.4 years ago by Jacob Michaelson320
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Comment: C: GOstats and GenePix arrays
... I hadn't thought of going through the trouble of making a custom annotation package. Last time I tried making one was quite a while back and it was quite a pain. I'm sure things work more smoothly now, but by looking at GOHyperG I realized all I really need is phyper and the appropriate GO mapping ...
written 13.4 years ago by Jacob Michaelson320
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Answer: A: GOstats and GenePix arrays
... Thanks Thomas. This is the kind of thing I was looking for. Thanks to all for their suggestions and encouragement. I know building a custom annotation package is the ideal scenario, but for "niche" organisms (ie not human, rat, mouse) this isn't always realistic. Annotation is often gathered by ...
written 13.4 years ago by Jacob Michaelson320
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Comment: C: GOstats and GenePix arrays
... Sean answered my question. By "similar function" I meant a function that was platform agnostic, as opposed to GOHyperG which assumes Affymetrix data. Really I'm not even writing a function, but just using the phyper function as part of a workflow in the place of GOHyperG. --Jake On Thu, 2006-0 ...
written 13.4 years ago by Jacob Michaelson320

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