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Ekta Jain
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50
@ekta-jain-5911
Last seen 10.2 years ago
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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---------
>>
>> -----------------------------
>>
>> Disclaimer:
>>
>> The information contained in this e-mail is intended
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>>
>> References
>>
>> 1. mailto:ekta.jain at teri.res.in
>> _______________________________________________
>> Bioconductor mailing list
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>
> _______________________________________________
> Bioconductor mailing list
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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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