Question: agilent zebrafish array annotation
0
gravatar for Georg Otto
11.1 years ago by
Georg Otto510
Georg Otto510 wrote:
Hi, I started to use the agilent zebrafish array and I am using bioconductor packages (limma and others) for the data analysis as I did already with the Affymetrix zebrafish array. I noticed that unlike for the Affymetrix zebrafish array, there is no annotation package for the Agilent zebrafish array, but there are packages for the Agilent human, mouse and rat arrays. Since I have some experience in creating custom annotation environments (e.g. using biomart) I would be willing to volunteer in generating an annotation package for the Agilent zebrafish array. However, it is not quite clear to me, how for example the mgug4104a.gb or other packages of this kind were generated. Reading the vignettes of the AnnBuilder and AnnotationDbi packages did not help me very much either. Therefor my question is: Is the package creation process documented somewhere? Is the code for the package generation available somewhere? As I said, I would be willing to generate the annotation package and contribute this to the community, but I do not know where to start. Best, Georg
ADD COMMENTlink modified 11.1 years ago • written 11.1 years ago by Georg Otto510
Answer: agilent zebrafish array annotation
0
gravatar for Marc Carlson
11.1 years ago by
Marc Carlson7.2k
United States
Marc Carlson7.2k wrote:
Georg Otto wrote: > Hi, > > I started to use the agilent zebrafish array and I am using > bioconductor packages (limma and others) for the data analysis as I > did already with the Affymetrix zebrafish array. I noticed that unlike > for the Affymetrix zebrafish array, there is no annotation package for > the Agilent zebrafish array, but there are packages for the Agilent > human, mouse and rat arrays. > > Since I have some experience in creating custom annotation > environments (e.g. using biomart) I would be willing to volunteer in > generating an annotation package for the Agilent zebrafish > array. However, it is not quite clear to me, how for example the > mgug4104a.gb or other packages of this kind were generated. Reading > the vignettes of the AnnBuilder and AnnotationDbi packages did not > help me very much either. > > Therefor my question is: Is the package creation process documented > somewhere? Is the code for the package generation available somewhere? > As I said, I would be willing to generate the annotation package and > contribute this to the community, but I do not know where to start. > > Best, > > Georg > > _______________________________________________ > 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 > > HiGeorg, Right now there are two styles of annotation package. The newer format is generated from code in the very latest bleeding edged version of AnnotationDbi (from the devel branch), and the older format is generated from AnnBuilder. It is preferable to use the newer code in AnnotationDbi, but this requires that your organism be supported first. As of right now, zebrafish is not a supported organism for the newer packages, but this is not set in stone. If you would be willing to work with me a little bit and be slightly more patient, we can try to rectify this situation together, but otherwise you are going to have to use the older AnnBuilder package to make your zebrafish packages. Making a vignette for AnnBuilder is mostly about calling the ABPkgBuilder() function with the correct parameters and using properly formatted inputs. Once zebrafish is a supported organism, the process for making a new package using AnnotationDbi's SQLForge functions would be very similar. I will be happy to help you with either of these processes. Marc
ADD COMMENTlink written 11.1 years ago by Marc Carlson7.2k
Answer: agilent zebrafish array annotation
0
gravatar for Georg Otto
11.1 years ago by
Georg Otto510
Georg Otto510 wrote:
Marc Carlson <mcarlson at="" fhcrc.org=""> writes: > Georg Otto wrote: >> Hi, >> >> I started to use the agilent zebrafish array and I am using >> bioconductor packages (limma and others) for the data analysis as I >> did already with the Affymetrix zebrafish array. I noticed that unlike >> for the Affymetrix zebrafish array, there is no annotation package for >> the Agilent zebrafish array, but there are packages for the Agilent >> human, mouse and rat arrays. >> >> Since I have some experience in creating custom annotation >> environments (e.g. using biomart) I would be willing to volunteer in >> generating an annotation package for the Agilent zebrafish >> array. However, it is not quite clear to me, how for example the >> mgug4104a.gb or other packages of this kind were generated. Reading >> the vignettes of the AnnBuilder and AnnotationDbi packages did not >> help me very much either. >> >> Therefor my question is: Is the package creation process documented >> somewhere? Is the code for the package generation available somewhere? >> As I said, I would be willing to generate the annotation package and >> contribute this to the community, but I do not know where to start. >> >> Best, >> >> Georg > > HiGeorg, > > Right now there are two styles of annotation package. The newer format > is generated from code in the very latest bleeding edged version of > AnnotationDbi (from the devel branch), and the older format is generated > from AnnBuilder. It is preferable to use the newer code in > AnnotationDbi, but this requires that your organism be supported first. > As of right now, zebrafish is not a supported organism for the newer > packages, but this is not set in stone. If you would be willing to work > with me a little bit and be slightly more patient, we can try to rectify > this situation together, but otherwise you are going to have to use the > older AnnBuilder package to make your zebrafish packages. > > Making a vignette for AnnBuilder is mostly about calling the > ABPkgBuilder() function with the correct parameters and using properly > formatted inputs. Once zebrafish is a supported organism, the process > for making a new package using AnnotationDbi's SQLForge functions would > be very similar. I will be happy to help you with either of these > processes. > > > Marc Hi Marc, thanks a lot for your quick answer and your offer to help! Of course I would be highly interested to have zebrafish in the list of supported organisms and I am willing to contribute to that. So I would like to hear what should be done and how I should start. From reading briefly through the AnnotationDbi documentation my understanding is, that a supported organism has a support database as a basis for the creation of annotation packages. Would it be a good idea to start creating such a support database for zebrafish, including data from NCBI, but maybe also Ensembl and ZFIN (the zebrafish database)? In the meantime (since I need to annotate the microarray result I have soon), I will start to create a simple old-style package using AnnBuilder. Georg
ADD COMMENTlink written 11.1 years ago by Georg Otto510
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