Hi Sabrina. I created a new thread as this is a new question. And a big one!
On 05/02/2009, at 6:06 AM, sabrina wrote: > Hi, Mark: > Quick question. I was looking at the example of creating cdfs from > scratch. I downloaded biomaRt , but not sure where to get or how to > create the exonBoundary file. Can you give me more information on > that? > Thanks! > > Sabrina First of all, you may want to start with the Ensembl-centric CDFs that Elizabeth has already made for the Mouse Exon 1.0 array. You can find these from the link at: http://groups.google.com/group/aroma-affymetrix/web/moex-1-0-st Creating custom CDFs for exon arrays is not an easy procedure and while we've (mostly Elizabeth) made some effort to document and share the code of how we have done it, we (or at least I) don't expect it to be bulletproof and it may require additional effort on your part. That said, to answer your question specifically, you'll need to make sure you get the exon coordinates (i.e. boundaries) when you download from Biomart. Here is one example of what I downloaded from Biomart way back when for the Human array: ----------- Ensembl Gene ID,Chromosome,Biotype,Exon Start (bp),Exon End (bp),Ensembl Exon ID,Constitutive Exon,Strand,Coding Start (bp),Coding End (bp) ENSG00000184895,Y,protein_coding, 2714896,2715740,ENSE00001494622,0,-1,2715030,2715644 ENSG00000184895,Y,protein_coding, 2715030,2715644,ENSE00001299380,0,-1,2715030,2715644 ENSG00000129824,Y,protein_coding, 2769527,2769668,ENSE00001494579,0,1,2769666,2769668 ENSG00000129824,Y,protein_coding, 2770206,2770283,ENSE00001159432,1,1,2770206,2770283 ENSG00000129824,Y,protein_coding, 2772118,2772298,ENSE00000891584,1,1,2772118,2772298 ----------- I did this from a query at http://www.ensembl.org/biomart/martview and downloaded the to a text file, but note that you should be able to download this directly to an R data.frame using the biomaRt package. These coordinates gets matched up to the coordinates in the probeset.csv file ... and so on and so on. HTH, Mark ------------------------------ Mark Robinson Epigenetics Laboratory, Garvan Bioinformatics Division, WEHI e: m.robin...@garvan.org.au e: mrobin...@wehi.edu.au p: +61 (0)3 9345 2628 f: +61 (0)3 9347 0852 ------------------------------ --~--~---------~--~----~------------~-------~--~----~ When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe from this group, send email to aroma-affymetrix-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en -~----------~----~----~----~------~----~------~--~---
