Annotation for Medicago array (Affy)
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Guido Hooiveld ★ 3.4k
@guido-hooiveld-2020
Last seen 3 days ago
Wageningen University, Wageningen, the …
Dear list, For a coworker we hybridized several Medicago arrays (Affymetrix). We are now at the stage of data analyses. Unfortunately, the annotation info provided by Affymetrix is limited, and a 'medicago.db' is missing at BioC. Therefore I would like to ask whether someone knows an alternative source for this. TIA, Guido ------------------------------------------------ Guido Hooiveld, PhD Nutrition, Metabolism & Genomics Group Division of Human Nutrition Wageningen University Biotechnion, Bomenweg 2 NL-6703 HD Wageningen the Netherlands tel: (+)31 317 485788 fax: (+)31 317 483342 internet: http://nutrigene.4t.com <http: nutrigene.4t.com=""/> email: guido.hooiveld@wur.nl [[alternative HTML version deleted]]
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Marc Carlson ★ 7.2k
@marc-carlson-2264
Last seen 6.2 years ago
United States
You should be able to just make a medicago annotation package in minutes. Just read the SQLForge vignette here: http://www.bioconductor.org/packages/devel/bioc/html/AnnotationDbi.htm l Marc Hooiveld, Guido wrote: > > Dear list, > For a coworker we hybridized several Medicago arrays (Affymetrix). We > are now at the stage of data analyses. Unfortunately, the annotation > info provided by Affymetrix is limited, and a 'medicago.db' is missing > at BioC. Therefore I would like to ask whether someone knows an > alternative source for this. > TIA, > Guido > > ------------------------------------------------ > Guido Hooiveld, PhD > Nutrition, Metabolism & Genomics Group > Division of Human Nutrition > Wageningen University > Biotechnion, Bomenweg 2 > NL-6703 HD Wageningen > the Netherlands > tel: (+)31 317 485788 > fax: (+)31 317 483342 > internet: http://nutrigene.4t.com <http: nutrigene.4t.com=""/> > email: guido.hooiveld at wur.nl > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > >
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Ana Conesa ▴ 340
@ana-conesa-2156
Last seen 8.1 years ago
Dear Guido The Blast2GO Functional Annotation Repository http://blast2go.bioinfo.cipf.es/b2gfar contains GO annotations for 17 non-model species Affymetrix GeneChip's, including Medicago. You can use the annotation simply as such or in combination with Blast2GO for analysis purposes (enrichment,visualization and so on) Cheers Ana > > >---- Mensaje Original ---- >De: Guido.Hooiveld at wur.nl >Para: bioconductor at stat.math.ethz.ch >Asunto: RE: [BioC] Annotation for Medicago array (Affy) >Fecha: Thu, 19 Feb 2009 22:46:38 +0100 > >> >>Dear list, >>For a coworker we hybridized several Medicago arrays (Affymetrix). >We >>are now at the stage of data analyses. Unfortunately, the annotation >>info provided by Affymetrix is limited, and a 'medicago.db' is >missing >>at BioC. Therefore I would like to ask whether someone knows an >>alternative source for this. >>TIA, >>Guido >> >>------------------------------------------------ >>Guido Hooiveld, PhD >>Nutrition, Metabolism & Genomics Group >>Division of Human Nutrition >>Wageningen University >>Biotechnion, Bomenweg 2 >>NL-6703 HD Wageningen >>the Netherlands >>tel: (+)31 317 485788 >>fax: (+)31 317 483342 >>internet: http://nutrigene.4t.com <http: nutrigene.4t.com=""/> >>email: guido.hooiveld at wur.nl >> >> >> [[alternative HTML version deleted]] >> >>_______________________________________________ >>Bioconductor mailing list >>Bioconductor at stat.math.ethz.ch >>https://stat.ethz.ch/mailman/listinfo/bioconductor >>Search the archives: http://news.gmane.org/gmane.science.biology.inf >ormatics.conductor >> ------------------------------------------- Ana Conesa, PhD Bioinformatics Department Centro de Investigaci?n Pr?ncipe Felipe Avda. Autopista Saler 16 46013 Valencia Spain http://bioinfo.cipf.es/aconesa ===========================================
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Hi, I have been analysing human and mouse gene ST chips using a combination of the Aroma package and the hugene10st.db and mogene10st.db annotation packages. Now I am attempting to perform the same on some rat gene ST chips but have unable to find the corresponding annotations. Why is there no ragene10st? thanks, Sebastien
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Hi Sebastien, We have just never had anyone ask for one before. However, you can make a package for yourself if you follow the instructions in the SQLForge vignette in the AnnotationDbi package: http://www.bioconductor.org/packages/devel/bioc/html/AnnotationDbi.htm l Please let me know if you have further questions regarding this. Marc Sebastien Gerega wrote: > Hi, > I have been analysing human and mouse gene ST chips using a > combination of the Aroma package and the hugene10st.db and > mogene10st.db annotation packages. Now I am attempting to perform the > same on some rat gene ST chips but have unable to find the > corresponding annotations. Why is there no ragene10st? > thanks, > Sebastien > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >
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Hi Marc and thanks for your help. I've had a look at the SQLForge vignette and there are still a couple issues that are unclear to me. Firstly, for the Rat Gene ST arrays is it possible to use any of the annotation files from the Affymetrix site as input for makeRATCHIP_DB in AnnotationDbi? If not, and the list of probes has to be manually created what is the best way to go about doing this? thanks again, Sebastien Marc Carlson wrote: > Hi Sebastien, > > We have just never had anyone ask for one before. However, you can make > a package for yourself if you follow the instructions in the SQLForge > vignette in the AnnotationDbi package: > > http://www.bioconductor.org/packages/devel/bioc/html/AnnotationDbi.h tml > > Please let me know if you have further questions regarding this. > > Marc > > > Sebastien Gerega wrote: > >> Hi, >> I have been analysing human and mouse gene ST chips using a >> combination of the Aroma package and the hugene10st.db and >> mogene10st.db annotation packages. Now I am attempting to perform the >> same on some rat gene ST chips but have unable to find the >> corresponding annotations. Why is there no ragene10st? >> thanks, >> Sebastien >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> > > >
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Hi Sebastien, The affy parameter is just a shortcut for affymetrix expression arrays. If you want to use that parameter, then you can download the appropriate annotation library file from Affymetrix website (which you probably have to get anyhow), just point to it in the parameter and then call the function. What SQLforge will then try to do is to parse this file by removing from it only the probeset IDs and the entrez gene, refseq IDs and unigene IDs from the file in order to sort out what all these genes are and thus generate the files that are described in the vignette from this affymetrix file. This will work as long as this particular annotation file is formatted similarly to what has come before. But, really this parameter is purely for convenience and not at all necessary to using SQLForge. A lot of people use affy, so I just added this to make it easier for that majority of users. You almost as easily can just grab that same Affymetrix annotation library file and make the tab delimited files that I described yourself. All you really need is a file that tells the gene identity of the different probesets. So you can ignore the vast majority of the data in the file. If you have that, then you have all that you really need to proceed. For most platforms this just means selecting out tow of the columns and then creating a tab file from those. Then you have to feed such a file to your function. Please let me know if you have more questions, Marc Sebastien Gerega wrote: > Hi Marc and thanks for your help. I've had a look at the SQLForge > vignette and there are still a couple issues that are unclear to me. > Firstly, for the Rat Gene ST arrays is it possible to use any of the > annotation files from the Affymetrix site as input for makeRATCHIP_DB > in AnnotationDbi? If not, and the list of probes has to be manually > created what is the best way to go about doing this? > thanks again, > Sebastien > > > Marc Carlson wrote: >> Hi Sebastien, >> >> We have just never had anyone ask for one before. However, you can make >> a package for yourself if you follow the instructions in the SQLForge >> vignette in the AnnotationDbi package: >> >> http://www.bioconductor.org/packages/devel/bioc/html/AnnotationDbi. html >> >> Please let me know if you have further questions regarding this. >> >> Marc >> >> >> Sebastien Gerega wrote: >> >>> Hi, >>> I have been analysing human and mouse gene ST chips using a >>> combination of the Aroma package and the hugene10st.db and >>> mogene10st.db annotation packages. Now I am attempting to perform the >>> same on some rat gene ST chips but have unable to find the >>> corresponding annotations. Why is there no ragene10st? >>> thanks, >>> Sebastien >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >>> >> >> >> > >
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Hi Marc, I guess the problem lies in the fact that I don't know which Annotation file to use. I can't seem to find any that have the appropriate columns. What files were used to generate mogene10st.db and hugene10st.db ? I can find appropriate annotations for Affy 3' arrays but not for the Gene St ones.... thanks again, Sebastien Marc Carlson wrote: > Hi Sebastien, > > The affy parameter is just a shortcut for affymetrix expression arrays. > If you want to use that parameter, then you can download the appropriate > annotation library file from Affymetrix website (which you probably have > to get anyhow), just point to it in the parameter and then call the > function. What SQLforge will then try to do is to parse this file by > removing from it only the probeset IDs and the entrez gene, refseq IDs > and unigene IDs from the file in order to sort out what all these genes > are and thus generate the files that are described in the vignette from > this affymetrix file. This will work as long as this particular > annotation file is formatted similarly to what has come before. But, > really this parameter is purely for convenience and not at all necessary > to using SQLForge. A lot of people use affy, so I just added this to > make it easier for that majority of users. > > You almost as easily can just grab that same Affymetrix annotation > library file and make the tab delimited files that I described > yourself. All you really need is a file that tells the gene identity of > the different probesets. So you can ignore the vast majority of the > data in the file. If you have that, then you have all that you really > need to proceed. For most platforms this just means selecting out tow > of the columns and then creating a tab file from those. Then you have > to feed such a file to your function. > > Please let me know if you have more questions, > > > Marc > > > > > > Sebastien Gerega wrote: > >> Hi Marc and thanks for your help. I've had a look at the SQLForge >> vignette and there are still a couple issues that are unclear to me. >> Firstly, for the Rat Gene ST arrays is it possible to use any of the >> annotation files from the Affymetrix site as input for makeRATCHIP_DB >> in AnnotationDbi? If not, and the list of probes has to be manually >> created what is the best way to go about doing this? >> thanks again, >> Sebastien >> >> >> Marc Carlson wrote: >> >>> Hi Sebastien, >>> >>> We have just never had anyone ask for one before. However, you can make >>> a package for yourself if you follow the instructions in the SQLForge >>> vignette in the AnnotationDbi package: >>> >>> http://www.bioconductor.org/packages/devel/bioc/html/AnnotationDbi .html >>> >>> Please let me know if you have further questions regarding this. >>> >>> Marc >>> >>> >>> Sebastien Gerega wrote: >>> >>> >>>> Hi, >>>> I have been analysing human and mouse gene ST chips using a >>>> combination of the Aroma package and the hugene10st.db and >>>> mogene10st.db annotation packages. Now I am attempting to perform the >>>> same on some rat gene ST chips but have unable to find the >>>> corresponding annotations. Why is there no ragene10st? >>>> thanks, >>>> Sebastien >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at stat.math.ethz.ch >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> >>>> >>>> >>> >>> >> > > >
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Well one way is to navigate Affymetrix's website and grab the annotation file http://www.affymetrix.com/support/technical/annotationfilesmain.affx Or you could also use Martin Morgans clever AffyCompatible package which will let you get the data you need more directly. ##The 2nd approach would go something like this (adapting from Martins Vignette): library(AffyCompatible) password <- "your_psswd" rsrc <- NetAffxResource(user="you at someplace.com", password=password) head(names(rsrc)) affxDescription(rsrc[["RaGene-1_0-st-v1"]]) annos <- rsrc[["RaGene-1_0-st-v1"]] annos sapply(affxAnnotation(annos), force) anno <- rsrc[["RaGene-1_0-st-v1", "Probeset Annotations, CSV Format"]] fl <- readAnnotation(rsrc, annotation=anno, content=FALSE) fl conn <- unz(fl, "RaGene-1_0-st-v1.na27.2.rn4.probeset.csv") ##Then get a dataframe with the contents of the file in it df = read.table(conn, header=TRUE, skip=18, sep=",") Marc Sebastien Gerega wrote: > Hi Marc, > I guess the problem lies in the fact that I don't know which > Annotation file to use. I can't seem to find any that have the > appropriate columns. What files were used to generate mogene10st.db > and hugene10st.db ? I can find appropriate annotations for Affy 3' > arrays but not for the Gene St ones.... > thanks again, > Sebastien > > > Marc Carlson wrote: >> Hi Sebastien, >> >> The affy parameter is just a shortcut for affymetrix expression >> arrays. If you want to use that parameter, then you can download the >> appropriate >> annotation library file from Affymetrix website (which you probably have >> to get anyhow), just point to it in the parameter and then call the >> function. What SQLforge will then try to do is to parse this file by >> removing from it only the probeset IDs and the entrez gene, refseq IDs >> and unigene IDs from the file in order to sort out what all these genes >> are and thus generate the files that are described in the vignette from >> this affymetrix file. This will work as long as this particular >> annotation file is formatted similarly to what has come before. But, >> really this parameter is purely for convenience and not at all necessary >> to using SQLForge. A lot of people use affy, so I just added this to >> make it easier for that majority of users. >> You almost as easily can just grab that same Affymetrix annotation >> library file and make the tab delimited files that I described >> yourself. All you really need is a file that tells the gene identity of >> the different probesets. So you can ignore the vast majority of the >> data in the file. If you have that, then you have all that you really >> need to proceed. For most platforms this just means selecting out tow >> of the columns and then creating a tab file from those. Then you have >> to feed such a file to your function. >> >> Please let me know if you have more questions, >> >> >> Marc >> >> >> >> >> >> Sebastien Gerega wrote: >> >>> Hi Marc and thanks for your help. I've had a look at the SQLForge >>> vignette and there are still a couple issues that are unclear to me. >>> Firstly, for the Rat Gene ST arrays is it possible to use any of the >>> annotation files from the Affymetrix site as input for makeRATCHIP_DB >>> in AnnotationDbi? If not, and the list of probes has to be manually >>> created what is the best way to go about doing this? >>> thanks again, >>> Sebastien >>> >>> >>> Marc Carlson wrote: >>> >>>> Hi Sebastien, >>>> >>>> We have just never had anyone ask for one before. However, you can >>>> make >>>> a package for yourself if you follow the instructions in the SQLForge >>>> vignette in the AnnotationDbi package: >>>> >>>> http://www.bioconductor.org/packages/devel/bioc/html/AnnotationDb i.html >>>> >>>> >>>> Please let me know if you have further questions regarding this. >>>> >>>> Marc >>>> >>>> >>>> Sebastien Gerega wrote: >>>> >>>> >>>>> Hi, >>>>> I have been analysing human and mouse gene ST chips using a >>>>> combination of the Aroma package and the hugene10st.db and >>>>> mogene10st.db annotation packages. Now I am attempting to perform the >>>>> same on some rat gene ST chips but have unable to find the >>>>> corresponding annotations. Why is there no ragene10st? >>>>> thanks, >>>>> Sebastien >>>>> >>>>> _______________________________________________ >>>>> Bioconductor mailing list >>>>> Bioconductor at stat.math.ethz.ch >>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>> Search the archives: >>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>> >>>>> >>>> >>> >> >> >> > >
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