User: Ariel Grostern

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Posts by Ariel Grostern

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Resend: altcdfenvs: mapping probes and creating new probe sets: guidance requested
... Hello, I am using R 2.10.0. The sessionInfo data is below at the end of this message. I am using Ubuntu 10.04. I am attempting to re-annotate custom Affy PM-only chip using a new gene-annotation for my prokaryotic genome. I have gotten stuck on altcdfenvs, however. What I have done so far: 1. Change ...
cdf probe affy altcdfenvs written 8.0 years ago by Ariel Grostern80
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altcdfenvs: mapping probes and creating new probe sets: guidance requested
... Hello, I am using R 2.10.0. The sessionInfo data is below at the end of this message. I am using Ubuntu 10.04. I am attempting to re-annotate custom Affy PM-only chip using a new gene-annotation for my prokaryotic genome. I have gotten stuck on altcdfenvs, however. What I have done so far: 1. ...
cdf probe affy altcdfenvs written 8.0 years ago by Ariel Grostern80 • updated 8.0 years ago by James W. MacDonald50k
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Comment: C: AnnotationDbi:makeProbePackage for PM-only chips....getting closer.....now error
... Hi James, That worked well. Thanks for your help, Ariel On Tue, 28 Jun 2011 10:05:51 -0400, "James W. MacDonald" wrote: > Hi Ariel, > > Use > > makeProbePackage("cb1190a520768f", > datafile=gzfile(filename,open="r"),outdir=outdir,maintainer=me,species =species, > version="1.0 ...
written 8.0 years ago by Ariel Grostern80
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AnnotationDbi:makeProbePackage for PM-only chips....getting closer.....now error in installation of probe package
... Hello, I am using R 2.10.0. The sessionInfo data is below at the end of this message. I am using Ubuntu 10.04. I am trying to make a probe package for a PM only Affy chip. I have altered the code for AnnotationDbi's makeProbePackage.R to not look for MM probes (see code pasted below). Then I ins ...
cdf probe affy annotationdbi written 8.0 years ago by Ariel Grostern80 • updated 8.0 years ago by James W. MacDonald50k
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Converting makeProbePackage in AnnotationDbi to permit PM-only arrays
... Hi, I am attempting to adapt the makeProbePackage function in AnnotationDbi to permit me to make a probe package for my PM-only Affy array, so that I can then use altcdfenvs to re-annotate the probes. My probe sequence file is set up exactly as the normal tab-limited PM/MM file. >From examining ...
cdf probe affy altcdfenvs written 8.0 years ago by Ariel Grostern80
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Follow-up: AnnotationDbi and makeProbePackage for PM-only Affy chips
... Hello again, I am following on my recent post regarding trying to make a probe package database for a custom, PM-only Affy microarray. I have found further discussions at https://stat.ethz.ch/pipermail/bioconductor/2007-February/016083.html and https://stat.ethz.ch/pipermail/bioconductor/2005-Septem ...
microarray affy annotationdbi written 8.0 years ago by Ariel Grostern80
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A circular problem: re-annotation of custom PM only probes
... Hello, I would like to re-annotate probes for a custom PM-only chip. I tried using altcdfenvs, but discovered that I first needed a make a probes database for my CDF library. To do this I tried using makeProbePackage, only to discover that the package matchprobes does not accept that my probes are P ...
cdf matchprobes written 8.0 years ago by Ariel Grostern80 • updated 8.0 years ago by Marc Carlson7.2k
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Re-annotation of probes for an Affy custom microarray
... Hello, I have a custom Affy Genechip that was designed using a draft version of a bacterial genome. We now have the finished version of the genome sequence available, so I would like to re-annotate the microarray probes to reflect the new genome sequence and gene numbering system. This problem app ...
annotation cdf affy written 8.0 years ago by Ariel Grostern80 • updated 8.0 years ago by Laurent Gautier2.2k

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