[BioC] Add new affy organism platform

Thu May 9 07:12:45 CEST 2013

Dear All,
Sorry for the late reply. I went underground for a bit. Thanks Marc, i did
try the cdf option since affymetrix did provide a .cdf file for rice. I was
however unable to annotate for gene names etc for the probe IDs using the
cdf environment in the way i would do using any .db package. Maybe i am
missing something but there must be a way to get this annotation from the
cdf file too, right?

I do not have the sql files for this rice microarray package but the .csv
annotation file which has the probe annotations, I can use this file in R
and annotate but at times its much easier and straightforward to annotate
from an in-built R package especially when performing differential gene
expression since you can then just fit the annotation on the differentially
expressed probes.

Is it possible to built a new .db package using a .csv file or would it
please be possible to obtain annotation from a cdf environment?

Thank you and Regards,
Ekta Jain
Research Analyst
Biotechnology and Bio-resources Division
The Energy and Resources Institute, India Habitat Centre
Lodhi Road, New Delhi - 110033
#09958818853
ekta.jain at teri.res.in

  From:       "James W. MacDonald" <jmacdon at uw.edu>                                                                    

  To:         Marc Carlson <mcarlson at fhcrc.org>,                                                                       

  Cc:         bioconductor at r-project.org                                                                               

  Date:       04/30/2013 05:13 AM                                                                                      

  Subject:    Re: [BioC] Add  new affy organism platform                                                               

  Sent by:    bioconductor-bounces at r-project.org                                                                       

Hi Marc,

My understanding is that you can't use SQLForge to create a chip-level
.db package unless there is a corresponding db0 package. Is that not
true? In this case the OP wants a rice.db package - is there an easy way
to make such a beast without a corresponding db0 package? Perhaps using
the makeOrgPackageFromNCBI?

Best,

Jim

On 4/29/2013 6:26 PM, Marc Carlson wrote:
> Hi Ekta,
>
> There are many different kinds of annotation packages in
> Bioconductor.  Which kind did you mean?  A .db package?  A .cdf
> package?  Maybe something else?
>
> There is a vignette that can help you to make a .db package here
> called "SQLForge: An easy way to create a new annotation package with
> a standard database schema.":
>
>
http://www.bioconductor.org/packages/release/bioc/html/AnnotationForge.html

>
>
> If it's a cdf package, then you should probably look here:
>
> http://www.bioconductor.org/packages/release/bioc/html/makecdfenv.html
>
>
> Hope this helps,
>
>
>   Marc
>
>
>
>
> On 04/28/2013 06:49 AM, Ekta Jain wrote:
>>     Dear All,
>>
>>     The affy platform annotation packages available in bioconductor
>> do not have
>>     "rice" included. Is there a way i can still use this in R?
>>
>>     Any suggestions would be highly appreciated.
>>
>>     Thank you
>>
>>     Ekta Jain
>>
>>     Research Analyst
>>     Biotechnology and Bio-resources Division
>>     The Energy and Resources Institute, India Habitat Centre
>>     Lodhi Road, New Delhi - 110033
>>     #09958818853
>>     [1]ekta.jain at teri.res.in
>>
>>
>>
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>>
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>>
>>     1. mailto:ekta.jain at teri.res.in
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--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099

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