Hi Mark Thank you very much. I have managed to successfully install aroma.affymetrix into R now. I was wandering however, with the spatial plots. Are the examples of the spatial plots that are on the google.groups page of the foreground and if so how can I compare it to the background?
Also for the density plots I want to generate a boxplot with the x axis representing the different arrays (I'm using the data set that is shown as an example on the google groups for the HuGene 1.0 ST array) and the y axis represents the log2 probe intensities. Do you know how I can do this? Thank you Cathy On Tue, Apr 21, 2009 at 7:16 AM, Mark Robinson <mrobin...@wehi.edu.au>wrote: > > Hi Cathy. > > Assuming aroma.affymetrix has installed correctly (somewhere on your > machine), it would seem that your R environment simply doesn't know > where to look for it. > > My guess is that if you call: > > .libPaths() > > ... the directory (or directories) that you see do NOT include the > place where aroma.affymetrix was installed. > > If you are using unix, you might look into setting your R_LIBS > environment variable. I don't know what to do in Windoze, but you > might check: > > http://cran.r-project.org/doc/manuals/R-admin.html#Installing-packages > > Hope that helps. > Mark > > > On 20/04/2009, at 11:45 PM, CathyMitchell wrote: > > > > > Hi, > > I am having some trouble installing "aroma.affymetrix" in the 2.9.0 > > version of R. When I use: > > > > source("http://www.braju.com/R/hbLite.R";) > > hbInstall("aroma.affymetrix") > > > > it seems to work fine and then tells me to restart R. However when i > > close that session and reopen another R session and call library > > (aroma.affymetrix) is says there is no aroma.affymetrix package. Is > > there something else I need to do? > > > > > > > ------------------------------ > 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 > ------------------------------ > > > > > > > > -- Cathrine Mitchell --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
