Add new affy organism platform
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Ekta Jain ▴ 50
@ekta-jain-5911
Last seen 7.1 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 >> >> >> ---------------------------------------------------------------------- --------- >> >> ----------------------------- >> >> Disclaimer: >> >> The information contained in this e-mail is intended >> for...{{dropped:12}} >> >> References >> >> 1. mailto:ekta.jain at teri.res.in >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099 _______________________________________________ Bioconductor mailing list Bioconductor at r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor ---------------------------------------------------------------------- -------------------------------------- Disclaimer: The information contained in this e-mail is intended for the person or entity to which it is addressed, and it may contain confidential and/or privileged material. Any review or other use of this mail or taking any action based on it by persons or entities other than the intended recipient is strictly prohibited. If you receive this e-mail by mistake, please contact the sender, and delete all copies of this mail.This e-mail has been scanned and verified by McAfee SaaS Email Security, formerly MX Logic.
Microarray Annotation Organism cdf db0 probe annotate affy Microarray Annotation cdf • 561 views
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Marc Carlson ★ 7.2k
@marc-carlson-2264
Last seen 5.1 years ago
United States
On 04/29/2013 04:07 PM, James W. MacDonald wrote: > 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 > No unfortunately that's correct. I had overlooked that he was working with rice. So a chip level package is not currently possible without a corresponding .db0. But he can probably still make an organism level package for rice by calling makeOrgPackageFromNCBI() (from the AnnotationForge package). Marc > > > 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/AnnotationFo rge.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 >>> >>> >>> ------------------------------------------------------------------ ------------- >>> >>> ----------------------------- >>> >>> Disclaimer: >>> >>> The information contained in this e-mail is intended >>> for...{{dropped:12}} >>> >>> References >>> >>> 1. mailto:ekta.jain at teri.res.in >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >
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