Hi George,

Sorry I haven't been able to respond - I've been extremely busy. It's 
actually better to post questions like this to the BioC list instead 
of to one poster directly - you might get a more timely response, and 
it's good to have the response in the archives so other people can 
access it. Your error message is pretty simple - you don't have 
package mpauta520274cdfprobe. I'm guessing this is a custom Affy 
array, so in addition to the mpaut1a520274fcdf package, you'll need a 
mpaut1a520274fprobe package to be able to use the RemoveProbes 
function "as is" and other functions like gcrma(). I forget off the 
top of my head what you need to do to make the probe package, so 
perhaps others will comment. If you can't make the probe package and 
only want to remove entire probe sets, then the code of RemoveProbes 
might be able to be modified to work without the probe package. 
Unfortunately, I won't have time for a couple of weeks to look at it. 
Feel free to hack it all you want if you can!  Sorry I can't be of 
more help right now...

Jenny

P.S. What's going on with your scans that you are getting "NA" values 
for individual probes? That's very odd!

At 05:48 PM 1/12/2010, George Roberts wrote:
>Dr. Drnevich,
>
>I would like to use your code 
><https://stat.ethz.ch/pipermail/bioconductor/2008-September/024296.html>https://stat.ethz.ch/pipermail/bioconductor/2008-September/024296.html 
>to remove some probesets that are causing "NA" values resulting in 
>errors. My CDF is "MPAUT1a520274F.CDF". I get the following error messages:
>
> > RemoveProbes(listOutProbes=NULL, listOutProbeSets="
>+ 1415670_at
>+ 1415671_at
>+ 1415672_at
>+ ", cleancdf)
>Loading required package: mpaut1a520274fcdfcdf
>Loading required package: mpaut1a520274fcdfprobe
>Error in get(probepackagename) :
>   object 'mpaut1a520274fcdfprobe' not found
>In addition: Warning messages:
>1: In library(package, lib.loc = lib.loc, character.only = TRUE, 
>logical.return = TRUE,  :
>   there is no package called 'mpaut1a520274fcdfcdf'
>2: In library(package, lib.loc = lib.loc, character.only = TRUE, 
>logical.return = TRUE,  :
>   there is no package called 'mpaut1a520274fcdfprobe'
>
>Thanks,
>George Roberts
>Wayne State University

Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

330 ERML
1201 W. Gregory Dr.
Urbana, IL 61801
USA

ph: 217-244-7355
fax: 217-265-5066
e-mail: drnevich@illinois.edu 
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