User: Jeffrey Rasmussen

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14 years, 5 months ago
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r******@u.washington.edu

Posts by Jeffrey Rasmussen

<prev • 10 results • page 1 of 1 • next >
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Answer: A: Limma, get the ranking position of a specific gene...
... Hi, Is there a citation for GOstats other than > citation(package="GOstats") To cite package GOstats in publications use: R. Gentleman (2005). GOstats: Tools for manipulating GO and microarrays. R package version 1.1.3. Also, the only publication I could find using GOstats & Rgraphv ...
written 14.5 years ago by Jeffrey Rasmussen100
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Comment: C: AnnBuilder questions...
... Hi all, My goal is to discover regions with multiple adjacent genes coordinately regulated. Are there any packages that would allow one to test for genomic loci that are overrepresented in a subset of genes versus the remaining genes on the chip? I have tried using the geneplotter package to visual ...
written 14.6 years ago by Jeffrey Rasmussen100
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Comment: C: ygs98
... Hi Christina, Are you using the latest version of GOstats? I had a similar problem sometime ago, but I believe the newer versions of GOstats (>1.6.5) have a workaround. See this old thread: http://files.protsuggest.org/biocond/html/6590.html Good luck, Jeff. On Fri, 21 Jan 2005, Christina Ken ...
written 14.8 years ago by Jeffrey Rasmussen100
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Answer: A: Problems with heatmap on genes...
... Hi Giulio, If you have access to Adobe Illustrator, you could write your heatmap to a postscript file using postscript() and then open and edit the file in Illustrator. I've found that in many cases this is much easier than wrangling with the plotting parameters in R, in particular when it comes to ...
written 15.0 years ago by Jeffrey Rasmussen100
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Missing GO terms in GOLOCUSID2GO
... Using GO 1.6.5 the following code produces a list of GO terms that are annotated as being connected with a certain LL id, but have their "Ontology" slot listed as "NA" (presumably because they are missing from GOTERM and the other GO* objects): library(GO) ll2go <- as.list.environment(GOLOCUSID2 ...
go written 15.1 years ago by Jeffrey Rasmussen100 • updated 15.1 years ago by rgentleman5.5k
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Comment: C: moe430v2 annotation package
... Hi James, Thanks for the suggestion, that seemed to do the trick. Note that the package is apparently called "moe430v2," which seems to be inconsistent with how the probe and cdf packages are named ("mouse4302"). Jeff. __________________________________ Jeffrey Rasmussen Research Consultant, Bioin ...
written 15.1 years ago by Jeffrey Rasmussen100
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moe430v2 annotation package
... I am trying to build an annotation package for Affy's Moe430 2.0 array (since it does not appear to be available under the metadata section) and I am wondering if my approach is the same as is used to build the "official" metadata packages. What I did was to simply use the annotation available from ...
annotation moe430a moe430b probe annbuilder written 15.1 years ago by Jeffrey Rasmussen100 • updated 15.1 years ago by John Zhang2.9k
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gcrma.bg.transformation missing in gcrma 1.1.0
... Hi, Using R 2.0.0-pre, gcrma 1.1.0, win2k: > library(gcrma) > atom.gcrma<-gcrma(atom.batch, type="fullmodel", fast=FALSE) Computing affinities.Done. Adjusting for optical effect.............Done. Adjusting for non-specific binding.Error in bg.adjust.fullmodel(pms[, i], mms[, i], pm.affini ...
gcrma written 15.3 years ago by Jeffrey Rasmussen100
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Iyer517 links broken
... Hi, I was hoping to play around with some time-course data in bioconductor, but to my dismay the links to the Iyer517 experimental data package appear to be broken. http://www.bioconductor.org/data/experimental/repos/Iyer517_1.0.zip http://www.bioconductor.org/data/experimental/repos/Iyer517_1.0.t ...
written 15.4 years ago by Jeffrey Rasmussen100 • updated 15.4 years ago by Jeff Gentry3.9k
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Comment: C: Warnings with Affy R 1.7.0
... Hi. Has anyone used the GenePlotter package on the mgu74Av2 affymetrix array? I have been unable to figure out how to extract the chromosomal location for the probesets from the data package for the u74 chip. Is this information built into that data package? If not, could someone please point me to ...
written 16.6 years ago by Jeffrey Rasmussen100

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