search for: pdinfobuild

Dear maintainer, I used bioconductor package, pdInfoBuilder, to make a microarray platform annotation package. I named this package, pd.pdinfo.gpl11164.ndf.txt. This "self-made package" is to be used with oligo package. Prior to using oligo package, I need to install the annotation package, pd.pdinfo.gpl11164.ndf.txt, and cannot just copy it...

...and limma packages. Now I am trying to analyze Rat Gene 10 st arrays and I would like to run RMA analysis and Smyth moderated t test on those arrays. Since no cdf official package is available for those arrays, after reading many of the questions and responses on this mailing list, I decided to use pdInfoBuilder, oligo and limma packages to run analysis. The problem is, at the end, I get expression and differential expression measured for all probe separately but not the calculated expression representing all probe of each gene. When I run RMA, I got only two steps, Background correcting and Normalizing...

...9;m guessing that it's changed somewhat because the PM arrays no longer have P/A and mismatches. I'm looking to build cdf and probe packages, if possible, but have yet to find any documentation on how to go about this using newer chips. I've also tried building pdInfo packages using pdInfoBuilder from CDF, csv annotation, and tab probe files downloaded from Affy, and makePdInfoPackage() fails like so: makePdInfoPackage(pkg, destDir="/home/mcininch/hthgu133pluspm") Creating package in /home/mcininch/hthgu133pluspm/pd.ht.hg.u133.plus.pm Error in data.frame(pmi = batchMat[isPm,...

My machine has 8GB memory. I had quit all other programs that might take a lot of memory when I try the script (before I post the first message in this thread). The cdf file is of only 741 MB. It is strange to me to see the error. On Mon, Dec 28, 2009 at 2:38 AM, Wolfgang Huber <whuber at embl.de> wrote: > Dear Peng Yu > > how big is the RAM of your computer? You could try with

I have recently upgraded to Ubuntu Gutsy and, for the first time, am using a 64-bit installation. After failing miserably to install R from source, not a problem for me in the past with a 32-bit install, I went the route of using the Debian Etch build. This went smoothly, but I am unable to update my numerous R and BioConductor packages, getting non-zero exit status errors on each package. Is