[this was sent to me offline. i've created a new thread and will try to respond in the next day or two.]
Begin forwarded message: > From: Frank <[email protected]> > Date: 2 March 2009 10:19:59 PM > To: Mark Robinson <[email protected]> > Subject: Re: FIRMA score > > Hi Mark, Hi everyboy, > > I would like to revive this thread and put the focus on the > visualization of "FIRMA-data" with GenomeGraphs. Maybe the vignette, > Mark has spoken of earlier, is already somewhere available? > > In any case I have some problems I could use help with. If you want to > use the ExonArray-class in GenomeGraphs you have to provide the > intensities (or whatsoever values you want to plot) for every probeset > and the end and start coordinates (and some more stuff). Like already > said in this thread before, you can find all this in the probeset > annotation files from affymetrix (link somewhere above) and you can > import this file with read.csv(...). > > But what I'm asking myself, how could you efficiently import this > file? For the HuEx its around 418 MB and contains over 1.4 million > lines. On my machine there is no way to import this file. Right now > I'm trying to build a function that works with chunks and that removes > all the "unnecessary" columns. But this looks not very convenient to > me. Isn't there any other way in R to extract only the rows of > interest, like you could do with grep under Unix? The grep and scan > functions in R don't seem to work on files that are not already read > in, or do I miss something? > > Maybe someone has a script to post here, that does nearly the > following: > Suppose you have an experiment with control/treatment and n chips for > each group. Your ResidualSet is stored in "rs", "csN" holds the > normalized intensities and "fs" the FirmaScores. For a given ensembl- > gene (e.g. "ENSG00000060237") the script should provide all the needed > values to create the object > exonarray<-new("ExonArray", intensity = ..., probeStart = , > probeEnd=..., probeId = ..., nProbes = ...) in GenomeGraphs (where > "intensity=..." should plot the FirmaScores for instance). > My feelings are, that one could do a lot of mistakes here when putting > all these values together. So some advice from someone who knows how > to do it, would we superb. > > Thanks in advance for your help and feedback, > Frank ------------------------------ Mark Robinson Epigenetics Laboratory, Garvan Bioinformatics Division, WEHI e: [email protected] e: [email protected] 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 [email protected] To unsubscribe from this group, send email to [email protected] For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en -~----------~----~----~----~------~----~------~--~---
