[BioC] removing probes from affybatch error
jmacdon at med.umich.edu
Wed Mar 31 19:31:34 CEST 2010
The AnnotationDbi package contains a function makeProbePackage() that
you can use to make probe packages.
Jenny Drnevich wrote:
> Hi George,
> I've never made a probe package either? Did you try searching the
> BioC archives for "make probe package"?
> Also, you forgot to post to the BioC list as well!
> At 08:40 AM 3/31/2010, George Roberts III wrote:
>> Hi Jenny,
>> I installed the .CDF package for my chips but still don't know how
>> to make a cdfprobe package and couldn't find any further info.
>> Thanks for your help,
>> On Sat, Jan 23, 2010 at 11:58 PM, George Roberts
>> <<mailto:groberts0429 at gmail.com>groberts0429 at gmail.com> wrote:
>> Hi Jenny,
>> Sorry for not posting in the BioC list, I will in the future; I
>> found the URL where you posted the previous email but don't know how
>> to reply to that thread so I replied to this email instead.
>> I spoke with the designers of the custom chip to find some insight
>> into the "NA" issue. All of the "NA" values were traced to a series
>> of probes that consist of only a single PM probe for each gene. They
>> were analyzed with GCOS and none gave "NA"; all gave a number. The
>> individual who performed the first analysis had no further insight
>> into whey R might have behaved this way. I want to exclude these
>> probes from my analysis in any event.
>> Thanks for pointing out that this error had to do with not
>> installing the .CDF package. I had loaded the .CDF environment in
>> the belief that it would be enough. Installing the .CDF package and
>> .CDFprobe package will be my next step.
>> Thank you very much for your help,
>> On Tue, Jan 19, 2010 at 9:38 AM, Jenny Drnevich
>> <<mailto:drnevich at illinois.edu>drnevich at illinois.edu> wrote:
>> 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...
>> 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
>>> 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'
>>> 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
>> ph: 217-244-7355
>> fax: 217-265-5066
>> e-mail: <mailto:drnevich at illinois.edu>drnevich at illinois.edu
> 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
> ph: 217-244-7355
> fax: 217-265-5066
> e-mail: drnevich at illinois.edu
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