User: rkakkar@uchicago.edu

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Posts by rkakkar@uchicago.edu

<prev • 10 results • page 1 of 1 • next >
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tkrplot in R2.0 on Mac OS X
... I am trying to get affylmGUI working in Rv2.0 on a Mac OS 10.3 machine. The only trouble I am having is with tkrplot. When I try and install it from source, the package installer, or from the "install.packages2" command, I get the following error: > install.packages2("tkrplot") Note: You did ...
affylmgui written 14.9 years ago by rkakkar@uchicago.edu100 • updated 14.9 years ago by James Wettenhall1000
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Installing Rv2.0.0 on MacOS 10.3.x
... My goal was to get Rv2.0.0 running on my MacOS 10.3.x machine with affy, annaffy, genefilter and chip libraries running (with widgets). The following is the protocol that worked (many thanks to R. Gentleman). Installed a fresh copy of Rv2.0.0 (uninstalled previous versions by removing the R applica ...
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Rv1.91 or v2.0.0 on MacOS 10.3.5
... This posting is regarding 2 problems, but all dealing with trying to run Bioconductor on MacOS 10.3.x. I initially tried to download and install Rv2.0.0 / Bioconductor. I included X11 upgrade during the installation. I used > source("http://www.bioconductor.org/getBioC.R") >getBioC("affy" ...
sage go kidney hgu95av2 hu6800 rae230a cdf biobase ruuid dyndoc annotate edd multtest written 15.0 years ago by rkakkar@uchicago.edu100 • updated 15.0 years ago by rgentleman5.5k
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Fwd: ttest genefilter 1.4.5 error on Rv2.0.0
... Begin forwarded message: > From: Rahul Kakkar > Date: October 25, 2004 8:24:34 AM CDT > To: Robert Gentleman > Subject: Re: [BioC] ttest genefilter 1.4.5 error on Rv2.0.0 > > Sir, > Yes. It was an error with eset$covariate. Thank you kindly for your > assistance. > ...
genefilter written 15.0 years ago by rkakkar@uchicago.edu100
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ttest genefilter 1.4.5 error on Rv2.0.0
... Ran into an error running genefilter 1.4.5 on Rv2.0.0 (windows XP). After updating to Rv2.0.0, Bioconductor was updated with getBioC (develOK=TRUE) without issue. Genefilter was updated manually with recently posted win32 build 1.4.5. error is the following: > tf1<-ttest(eset$mutant, p=.0 ...
cdf genefilter written 15.0 years ago by rkakkar@uchicago.edu100 • updated 15.0 years ago by rgentleman5.5k
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error using genefilter for ttest in Rv2.0.0
... Thanks for the win32 build of genefilter for Rv2.0. Have run into an error when using genefilter to run a t-test. Error seems to indicate genefilter is nor recognizing format of eset. Please advise. Thanks again. > data AffyBatch object size of arrays=1164x1164 features (42346 kb) cdf=HG-U1 ...
cdf genefilter written 15.0 years ago by rkakkar@uchicago.edu100
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genefilter and Rv2.0.0
... Attempting to load genefilter into Bioconductor on Rv2.0.0 (Windows). Rv2.0.0 seems to require update to developer releases of most Bioconductor packages as they would not load otherwise (used getBioC("all", develOK=TRUE) for this). However, genefilter seems to be at release 1.4.0, which will not lo ...
genefilter written 15.0 years ago by rkakkar@uchicago.edu100 • updated 15.0 years ago by rgentleman5.5k
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merging gene lists
... if i have two lists of differentially regulated genes (they could be from 2 different statistical tests, or differentially regulated genes in two treatment groups) which id like to compare, how would those with R/Bioconductor experience suggest i perform list comparisons to answer the following ques ...
written 15.8 years ago by rkakkar@uchicago.edu100 • updated 15.8 years ago by Sean Davis21k
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(no subject)
... i am trying to import a probe list into R for use in annaffy. i have used affy to generate an eset which i imported into SAM (MS Excel). After SAM permutation, I now have a list of probe ids (a csv file "probelist.csv") that id like to bring back into bioconductor to annotate. i created an object ...
probe affy annaffy written 15.8 years ago by rkakkar@uchicago.edu100
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Potential reposTools bug (was: simple error)
... getting same error as posted in "[BioC] Potential reposTools bug (was: simple error)" Follwing fresh install of R1.8.1, Bioconductor 1.3 (Windows XP), loading .cel data and executing "eset <- expresso (Data, widget=TRUE" / selecting methods via widget, R console indicates background correction, ...
repostools written 15.8 years ago by rkakkar@uchicago.edu100

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