User: lgautier@altern.org

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Posts by lgautier@altern.org

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Comment: C: observations on affyprobeminer
... > I was not clear in my original post, I filtered out duplicate entrez gene > IDs taking only the one with the lowest p-value. I see... Then there is really no simple answer to what you are observing; some of the probesets in the Affymetrix mapping are the result of combining information fro ...
written 11.1 years ago by lgautier@altern.org950
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Comment: C: filtered CDF file results in errors
... > Sebastien Gerega wrote: >> Hi, >> I am working on the yeast2 affymetrix chip and am trying to filter out >> all the s_pombe probes with the following code: >> >> library(altcdfenvs) >> bothcdf = wrapCdfEnvAffy(yeast2cdf, 496, 496, "yeast2cdf") >> pp = r ...
written 11.1 years ago by lgautier@altern.org950
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Answer: A: observations on affyprobeminer
... > I have recently explored the use of alternative CDFs from affyprobeminer (APM) or a 36 array dataset derived using the Affy rat2302 chipset. I used > both the Affy cdf and the transcript-level affyprobeminer cdf. I preprocessed using RMA, filtered using an A/P filter, and statistically analy ...
written 11.1 years ago by lgautier@altern.org950
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Comment: C: How can I see .C source code in affy package?
... Yeon-Ki Kim, Depending on what you want to do, the package preprocessCore might have what you are looking for. Some of the routines in the "affy" package were taken out to be placed in that package. Check the file: preprocessCore/src/qnorm.c Laurent > Download the source tarball from th ...
written 11.1 years ago by lgautier@altern.org950
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Answer: A: to create a random graph
... You need the package "graph": randomEGraph(graph) Random Edge Graph randomGraph(graph) Random Graph randomNodeGraph(graph) Generate Random Graph with Specified Degree Distribution > hi ,everyone > i want to create a random graph wi ...
written 11.2 years ago by lgautier@altern.org950
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Comment: C: Merging microarray datasets
... > Thanks to Adai and Eric, > > Well, I'm trying to bring back the discussion to the previous direction as > it apparently went to a different area : cross-platform integration. :) > I > was wondering about integration within the same platform ? an issue when > there are multiple ...
written 11.2 years ago by lgautier@altern.org950
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Answer: A: Creating the cusotm CDF file package in R - windows.
... Check http://www.murdoch-sutherland.com/Rtools/ > Hi All, > > I need to create CDF package for R- windows XP. Rafael Irizarry has > suggested that it is not easy. when I did it I got the following error > message. I have installed R-tools in my C:\.There is supposed to be a link & ...
written 11.2 years ago by lgautier@altern.org950
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Comment: C: a bug in hypergraph?
... Gunther, You can generally have an "embedded R" called from a C program. The R manual "R-extentions" (distributed with R, or at http://cran.r-project.org/doc/manuals/R-exts.pdf) will have some of the details. The functions or data structures you refer to are in R packages, and knowing a bit of R w ...
written 11.3 years ago by lgautier@altern.org950
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Answer: A: Restore lost mm probes in an altcdfenv?
... > Hi all, > Being an R novice I'm hoping someone in the community might have > already dealt with something of this sort. > > I'm trying to create an altcdfenv (or analogous package) remapping the > probes from a custom chip onto new gene sequences. I've read the > excelle ...
written 11.3 years ago by lgautier@altern.org950
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Comment: C: set.seed() in gcrma
... > Anderson, S. Keith scripsit: >> Pierre, >> I have not tried that. >> And yes, I would expect to obtain slightly different results with just shuffling the order of the CEL files. >> S. Keith Anderson >> -----Original Message----- >> From: Pierre Neuvial [mailt ...
written 11.3 years ago by lgautier@altern.org950

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