[aroma.affymetrix] Re: FIRMAGene
Dear Mark,
I'm wondering whether there is relationship between the array
quality, in terms of NUSE (and RLE?) plot, and the FIRMAGene scores.
Do you expect that a low quality array will show higher FIRMAGene
scores respect to a high quality array?
Indeed, from preliminary analysis, it seems that this is the case.
Thanks,
Ettore M.
On Jun 11, 3:10 pm, Mark Robinson wrote:
> Hi Nick.
>
> At present, FIRMAGene is not actually part of the aroma.affymetrix
> project, although it makes use of it. So, I will reply to this off
> the aroma.affymetrix mailing list, except to say that FIRMAGene is now
> hosted by R-forge. See the following link for details:
>
> http://bioinf.wehi.edu.au/folders/firmagene/
>
> When (and if) time permits, I plan to add FIRMAGene to
> aroma.affymetrix, so that it can share the same memory efficiency and
> mailing list support.
>
> Cheers,
> Mark
>
> On 11/06/2009, at 10:31 PM, nmcgli...@googlemail.com wrote:
>
>
>
>
>
> > Hello,
>
> > I have two questions regarding FIRMAGene:
>
> > 1. The same as the first in this thread: using the code from sup3.r
> > when I try to load the FIRMAGene library or execute the FIRMAGene
> > command I get the following errors:
>
> >> library(FIRMAGene)
> > Error in base::library(...) : there is no package called 'FIRMAGene'
>
> >> fg <- FIRMAGene(plm, idsToUse=u)
> > Error: could not find function "FIRMAGene"
>
> > I'm using aroma.affymetrix v1.1.0 with R2.9.0 on MacOSX 10.5.7
>
> > 2. I'm unsure of what this command is doing and how it needs to be
> > changed to accommodate my own data:
>
> > cls <- gsub("TisMap_","",gsub("_0[1-3]_v1_WTGene1","",getNames(cs)))
>
> > Many thanks,
>
> > Nick
>
> --
> Mark Robinson, PhD (Melb)
> 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
> --
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[aroma.affymetrix] Re: FIRMAGene
I have the following question. In the "sup3.R" file the probe level model fitting is realised using the instructions: plm <- RmaPlm(csNU) fit(plm, verbose=verbose) where csNU is an object obtained after background correction, quantile normalisation and conversion of the cdf to a "unique" version. I suppose that this approach should enable the exon-level analysis of the Gene 1.0 data, as required by FIRMAGene. However I don't understand where is the difference since the methods are the same as in the gene-level analysis of such data. Thanks, Ettore M. On May 29, 3:16 pm, rhizomorph wrote: > I have the same question as Ettore. I installed the aroma.affymetrix > package (and all supporting packages), but nowhere can I find a source > to download and install the FIRMAGene package that the "SUP3.R" script > clearly calls for. > > Rhizomorph. > > On May 29, 3:15 am, ettore mosca wrote: > > > Dear aroma.affymetrix developers, > > > I'm very interested in using Gene 1.0 ST platform for alternative > > splicing. I read in your paper "Differential splicing using > > whole-transcript microarrays" that FIRMAGene "is freely available as R > > package" but I can not load the library following the instruction in the > > third additional file "sup3.r" (I installed and loaded aroma.affymetrix > > successfully) > > > How do I install and load FIRMAGene library? > > > Thanks, > > > Ettore M. > > > -- > > Ettore M. > > >http://www.ettoremosca.it --~--~-~--~~~---~--~~ 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 -~--~~~~--~~--~--~---
[aroma.affymetrix] FIRMAGene
Dear aroma.affymetrix developers, I'm very interested in using Gene 1.0 ST platform for alternative splicing. I read in your paper "Differential splicing using whole-transcript microarrays" that FIRMAGene "is freely available as R package" but I can not load the library following the instruction in the third additional file "sup3.r" (I installed and loaded aroma.affymetrix successfully) How do I install and load FIRMAGene library? Thanks, Ettore M. -- Ettore M. http://www.ettoremosca.it --~--~-~--~~~---~--~~ 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 -~--~~~~--~~--~--~---
[aroma.affymetrix] Re: exon analysis of Human Gene 1.0 ST Array
Dear Mark,
I think that the manuscript you cited ("Differential splicing using
whole-transcript microarrays") has been published few days ago.
However, I can not load the library FIRMAGene. Is it already included
in the aroma.affymetrix package?
Congratulations for your work,
Best,
Ettore M.
On Apr 18, 5:12 am, "Mark Robinson" wrote:
> Hi Dick.
>
> Short answer is yes. I have a manuscript in press at BMC Bfx ... really
> just a minor modification of FIRMA. The software is mostly in place, but
> I want to make a few changes/enhancements before I release (and support)
> it.
>
> Cheers,
> Mark
>
>
>
> > Is there any capability in aroma or any plans to implement some type
> > of exon analysis, such as FIRMA, for the Human Gene 1.0 ST Arrays?
>
> > Thanks,
> > Dick
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