Hi, ----> Thanks for your response regarding mapping IMAGE clone IDs to unigene. I have some further questions I am not using Affymetrix arrays. This is why I don't think that downloading the "Annotation CSV" files will help me? It seems that in the examples on the vignettes that the starting point is a list containing Affymetrix probe id's and then Genbank accession numbers. My starting point is a list of clone id's. I will use the examples from the Bioconductor parsers and investigate creating my own parser. However, when it comes to the mapping of clone id to accession number is there something in Bioconductor that I can use? My next question would be could I use the function fileMuncher? Also, how do I find out more about functions while using Bioconductor? Other than looking at the code how can I find out more about ABPkgBuilder(which I will be doing)? Also, is there a way of 'running' a vignette so that you don't have to type everything in? A minor but important question. In R if you mistype a line like you are in the middle of typing a long if statement. What keys can you hit so that you can fix the if statement without retyping the whole if statement? >I am new to BioConductor and would appreciate advice with the following. >My goal is to take cloneID's from for example Human microarray 19K human >ESTs >and find out the corresponding accession number and subsequently Unigene >identifier. >I would like to keep a database of this information. You can download the "Annotation CSV" (or other format) for your chip from "http://www.affymetrix.com/analysis/download_center.affx". The file contains mappings to GenBank accession numbers, Unigene ids, and other information. ------------------------------------------------------- ----> I was following along the "How to use AnnBuilder" vignette and got to the end. I was not sure at the end on how to use the data package I had built. Where can I go to find out more information on how to use a data package and data packages in general? ------------------------------------------------------- ----> In your vignettes on AnnBuilder I can see that you are loading up your base file, specifying which sites to download data, then there are calls to parsers. For the next step I would like to know the main functions responsible for mapping. I would like to know if there are some functions I can use for mapping or ones I can look at to model after. ------------------------------------------------------- ----> Can you suggest a good resource for takig XML information and dumping it into a database? thanks very much, Annie.

>Thanks for your response regarding mapping IMAGE clone IDs to unigene. >I have some further questions >I am not using Affymetrix arrays. This is why I don't think that >downloading >the "Annotation CSV" files will help me? You are right. > >It seems that in the examples on the vignettes that the starting point is >a list containing Affymetrix probe id's and then Genbank accession numbers. >My starting point is a list of clone id's. I will use the examples from >the Bioconductor parsers and investigate creating my own parser. >However, when it comes to the mapping of clone id to accession number >is there something in Bioconductor that I can use? No, users are responsible for providing a file with the required mappings. > >My next question would be could I use the function fileMuncher? >Also, how do I find out more about functions while using Bioconductor? >Other than looking at the code how can I find out more about >ABPkgBuilder(which I will >be doing)? type ?function name (e. g. ?fileMuncher) will show the help page for the function. > >Also, is there a way of 'running' a vignette so that you don't have to type >everything in? library(tkWidgets) vExplorer() envokes a widget that allows users to explore the vignettes of installed packages without having to type the code. > >A minor but important question. In R if you mistype a line like you are in >the middle >of typing a long if statement. What keys can you hit so that you can fix >the if statement >without retyping the whole if statement? Why do'nt you type your code in a text editor and then cut/paste your code to R. > >>I am new to BioConductor and would appreciate advice with the following. >>My goal is to take cloneID's from for example Human microarray 19K human >>ESTs >>and find out the corresponding accession number and subsequently Unigene >>identifier. >>I would like to keep a database of this information. > >You can download the "Annotation CSV" (or other format) for your chip from >"http://www.affymetrix.com/analysis/download_center.affx". The file contains > >mappings to GenBank accession numbers, Unigene ids, and other information. > >------------------------------------------------------- >----> >I was following along the "How to use AnnBuilder" vignette and got to the >end. >I was not sure at the end on how to use the data package I had built. >Where can I go to find out more information on how to use a data package and >data packages in general? > >------------------------------------------------------- >----> >In your vignettes on AnnBuilder I can see that you are loading up your >base file, >specifying which sites to download data, >then there are calls to parsers. >For the next step I would like to know the main functions responsible for >mapping. >I would like to know if there are some functions I can use for mapping or >ones >I can look at to model after. > >------------------------------------------------------- >----> > >Can you suggest a good resource for takig XML information >and dumping it into a database? > > >thanks very much, >Annie. > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor

Hi, Thanks for your response. I have a few more questions... 1. I was following along the "How to use AnnBuilder" vignette and got to the end. I was not sure at the end on how to use the data package I had built. Where can I go to find out more information on how to use a data package and data packages in general? 2. In your vignettes on AnnBuilder I can see that you are loading up your base file, specifying which sites to download data, then there are calls to parsers. For the next step I would like to know the main functions responsible for mapping. I would like to know if there are some functions I can use for mapping or ones I can look at to model after. 3. Can you suggest a good resource for takig XML information and dumping it into a database? thanks very much, Annie.

> >Thanks for your response. I have a few more questions... > >1. I was following along the "How to use AnnBuilder" vignette and got to the >end. I was not sure at the end on how to use the data package I had built. >Where can I go to find out more information on how to use a data package and >data packages in general? Using hgu95av2 as an example, hgu95av2() shows a list of the environment objects contained with some quality control maesurements and ?hgu95av2 gives the data sources used to build the data package. Each environment object contained by the packages has a help file that can be shown by typing ?objectName (?hgu95av2SYMBOL). Common opertions for a given environment object include: ls(objectName) (ls(hgu95av2SYMBOL)) lookUp(keys, package, element) (lookUp(c("40576_f_at","1091_at"), "hgu95av2", "SYMBOL"). The developmental version of annotate is required) > >2. In your vignettes on AnnBuilder I can see that you are loading up your >base file, specifying which sites to download data, then there are calls to >parsers. >For the next step I would like to know the main functions responsible for >mapping. >I would like to know if there are some functions I can use for mapping or >ones I can look at to model after. fileMuncher is the one that does the mapping. But if you have your clones mapped to either GenBank, UniGene, LocusLink, or IMAGE ids, you can just use ABPkgBuilder to build the data package. > >3. Can you suggest a good resource for takig XML information >and dumping it into a database? Depending on what application language you will be using. For R, the XML package is useful. > >thanks very much, >Annie. > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor Jianhua Zhang Department of Biostatistics Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084