running exonmap package and chimp arrays
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Pete Shepard ▴ 240
@pete-shepard-3324
Last seen 8.4 years ago
Dear Bioconductor list, I am brand new to Bioconductor and am interested in looking at exon arrays. I have two questions: 1) In the "common workflows" section of the getting started section, it says that to use the exonmap package I need >=8GB of RAM, I have 2GB. Is there a way around this? 2) Also I would like to look at human exon arrays and chimp/primate exon arrays. I am wondering if Bioconductor has a list of exon sets and data that are available to users? Thanks [[alternative HTML version deleted]]
exonmap exonmap • 649 views
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@michal-okoniewski-3249
Last seen 8.4 years ago
Hi Pete, Technically, a lot of functionality of exonmap is for annotation processing. It means in practice that if you want to translate genes to exons and to probesets etc, you need a connection to X:MAP database that runs on MySQL . The >8G RAM requirement is related mainly to the summarization (RMA) of exon array AffyBatch objects. So the way around for your question 1) would be - to run summarization once elsewhere (where more RAM is available) and save the eSet object to a file, load it to your 2G computer connected to X:MAP and run all the exonmap pipelines for analysis. Just in case you may want to save pairwise comparison outcome objects too. Alternatively, you may summarize the data with xps package (it uses root.cern.ch schema to store the data outside the RAM), then use exonmap to analyze and visualize. As for 2) - I have not heard about dedicated chimp array, however there were attempts to run chimp RNA on human exon array (Affy chip has versions for Human, Mouse, Rat). Eg. a human tissue dataset was to be downloaded from Affy site. Cheers, Michal Pete Shepard wrote: > Dear Bioconductor list, > > I am brand new to Bioconductor and am interested in looking at exon arrays. > I have two questions: > > 1) In the "common workflows" section of the getting started section, it says > that to use the exonmap package I need >=8GB of RAM, I have 2GB. Is there a > way around this? > > 2) Also I would like to look at human exon arrays and chimp/primate exon > arrays. I am wondering if Bioconductor has a list of exon sets and data that > are available to users? > > Thanks > > [[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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