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 <mrobin...@wehi.edu.au> 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 > ------------------------------ --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
