I'm glad it worked. Hope the results are interesting, too! :-) Cheers, Norman On Fri, Jun 15, 2012 at 5:54 PM, Olli Kannaste <ojkann at="" utu.fi=""> wrote: > Yes, that sorted it out! Thanks for the tip. > > Cheers, > Olli > ________________________________________ > L?hett?j?: Norman Pavelka [normanpavelka at gmail.com] > L?hetetty: 15. kes?kuuta 2012 6:04 > Vastaanottaja: Olli Kannaste > Cc: bioconductor at r-project.org > Aihe: Re: FW: plgem > > Hi Olli, > > As I suspected, you are using a very old version of R and Bioconductor > (2008). Try downloading the latest version of R and re-install the > latest plgem package by typing: > > ?source("http://bioconductor.org/biocLite.R") > ?biocLite("plgem") > > Let me know if this solves the problem. > > Cheers, > Norman > > On Thu, Jun 14, 2012 at 4:52 PM, Olli Kannaste <ojkann at="" utu.fi=""> wrote: >> Hi Norman, >> >> Sure thing. Here is the output: >> >> R version 2.7.2 (2008-08-25) >> i386-pc-mingw32 >> >> locale: >> LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United Kingdom.1252;LC_MONETARY=English_United Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 >> >> attached base packages: >> [1] tools ? ? stats ? ? graphics ?grDevices utils ? ? datasets ?methods >> [8] base >> >> other attached packages: >> [1] plgem_1.12.0 ?MASS_7.2-44 ? Biobase_2.0.1 >> >> -- >> >> Thanks, >> Olli >> ________________________________________ >> L?hett?j?: Norman Pavelka [normanpavelka at gmail.com] >> L?hetetty: 14. kes?kuuta 2012 4:35 >> Vastaanottaja: Olli Kannaste >> Cc: bioconductor at r-project.org >> Aihe: Fwd: FW: plgem >> >> Dear Olli, >> >> Thanks for your email and your continued interest in plgem. From your >> error message it looks like there might be a version problem. Could >> you please send me the output of sessionInfo() ? >> I am also copying the Bioconductor mailing list, so the thread gets archived. >> >> Cheers, >> Norman >> >> -----Original Message----- >> From: Olli Kannaste [mailto:ojkann at utu.fi] >> Sent: Wednesday, 13 June, 2012 9:07 PM >> To: Norman Pavelka (SIgN) >> Subject: plgem >> >> Hi Norman, >> >> I approached you about 2.5 years ago regarding problems i was having >> with the plgem analysis. You were kind enough to provide me an R >> script, which automated the analysis. That worked fine and helped me a >> great deal. I am now trying plgem again using the script with some >> other data, and having some difficulties... I'm working on a different >> computer now and have installed the latest version of plgem. My guess >> is that for some reason the script is not working properly with the >> new plgem version. It lets me input my parameters and specify data >> files but fails to proceed right after that, generating the following >> error message: >> >> Error in run.plgem(get(expressionSetName), signLev = pVal, rank = 100, ?: >> ?unused argument(s) (trimAllZeroRows = TRUE, zeroMeanOrSD = "replace") >> >> Could you perhaps help me out with this one? I'm attaching the script >> and my input files in the message. >> >> Best regards, >> Olli