User: Justin Borevitz

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15 years, 5 months ago
Joined:
16 years, 4 months ago
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b*******@salk.edu

Posts by Justin Borevitz

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cdf vs probe package & Linux vs PC
... I've noticed that the order of probes in the 2 packages does not agree. At least for barley1 and ath1121501. Also the way probes are ordered in Linux and Rgui (PC) does not agree. It could be something with the alphabetizing of probsets names in the 2 versions. Its possible this is true for the ...
ath1121501 cdf probe affy written 15.5 years ago by Justin Borevitz90 • updated 15.4 years ago by Wolfgang Huber13k
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Comment: C: Re: Logit-t vs RMA
... Hi Jenny, your setup has several valid permutations which can be used to account for your setup and multiple testing. You can also try and estimate the proportion of genes different from the null. The FDR q value might be of more interest in this case. See "Statistical significance for genomewide ...
written 16.1 years ago by Justin Borevitz90
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Comment: C: Installation of ath1121501cdf
... The manual installation worked fine for me yesterday on linux RH9 after I had the same download error. This occurred when I tried to use justRMA() on some ATH1 .cel files when the ath1121501cdf had not been installed privously. Other packages (e.g. getBioC() ) do download fine on my system so there ...
written 16.2 years ago by Justin Borevitz90
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update.packages
... Great works now > update.packages(CRAN=getOption("BIOC")) trying URL `http://www.bioconductor.org/bin/windows/contrib/1.7/PACKAGES' Content type `text/plain' length 11255 bytes opened URL downloaded 10Kb affy : Version 1.2.28 in C:/R/rw1071/library Version 1.2.30 on CRAN Update (y/N)? y tryin ...
widgettools written 16.2 years ago by Justin Borevitz90
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Comment: C: errors in imageplot() in limma
... Similar problem as this morning with widgetTools, which is now fixed. I'm sure you are working on it. Update ran fine from linux. In WinXP R1.7.1 > update.packages(CRAN=getOption("BIOC")) trying URL `http://www.bioconductor.org/bin/windows/contrib/1.7/PACKAGES' Content type `text/plain' length ...
written 16.2 years ago by Justin Borevitz90
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Comment: C: com.braju.sma
... Justin http://naturalvariation.org We are having a little debate about whether RMA is using MM oligos at all. I know that PM.only is the method that calls the gene expression index, but Are MM intensities used in the calculation for the background correction? I thought I'd put this out to get th ...
written 16.3 years ago by Justin Borevitz90
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Comment: C: problems intalling bioconductor on windows NT
... I had this problem last night and this morning but I just tried again and its working now. You can run in R install.packages("Biobase",CRAN=getOption("BIOC")) install.packages("genefilter",CRAN=getOption("BIOC")) those were the ones that initially failed for me. Justin http://naturalvariation ...
written 16.3 years ago by Justin Borevitz90
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Answer: A: question about ath1121501cdf package
... Hi Wenlei, there are 2 commercial Arabidopsis arrays. One is ATH1 that has 22k genes, the other is the old one with 8k genes called AG. You have downloaded the wrong cdf package because the link is incorrect. You can download the Source for ATH1 from bioconductor and install it if you are set up ...
written 16.4 years ago by Justin Borevitz90
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Comment: C: change working directory command on command line
... Hi all great to be part of a highly active/responsive group! Has anyone else thought about spatial correction for affy arrays? Charles Berry and I have done some simple corrections using sliding windows, see Figure 1. http://www.genome.org/cgi/content/full/13/3/513/F1 or http://naturalvariation.org ...
written 16.4 years ago by Justin Borevitz90

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