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 >>>>> >>>>> >>>> >>> >> >> >> > >