Hello there, I am writing for a second time to ask for some help with a LimmaGUI error I am having. I am trying to load some BlueFuse results files into LimmaGUI. I am able to load the data in (seen in R window as being read in). I am using the other file type function in limmaGUI. I have no errors when reading the information in, and I am also able to create an M box plot with no normalization for all slides. The problem is that when I go to plot an M box plot with any combination of normalization (either within norm and/or between slide normalization) I get the following errors: Error: subscript out of bounds Then Error in assign ("MAwithinArrays", MA, limmaGUIenvironment) : Object "MA" not found. I am using R in Windows XP, version R 2.1.1 and LimmaGUI version 1.3.9 Please help.... Liz

Sorry that this probably isn't much help, but do you get the same errors when doing these plots via command line instead of the limma GUI? jon butchar On Monday 01 August 2005 04:29 pm, Brooke-Powell, Elizabeth wrote: > Hello there, > > I am writing for a second time to ask for some help with a LimmaGUI > error I am having. I am trying to load some BlueFuse results files > into LimmaGUI. I am able to load the data in (seen in R window as > being read in). I am using the other file type function in limmaGUI. > I have no errors when reading the information in, and I am also able > to create an M box plot with no normalization for all slides. The > problem is that when I go to plot an M box plot with any combination > of normalization (either within norm and/or between slide > normalization) I get the following errors: > > Error: subscript out of bounds > > Then > > Error in assign ("MAwithinArrays", MA, limmaGUIenvironment) : Object > "MA" not found. > > I am using R in Windows XP, version R 2.1.1 and LimmaGUI version > 1.3.9 > > Please help.... > > Liz > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor

hi! being a new bioconductor user I am not sure, wether I can help you, but you could try downloading and installing the TCL libraries, which the GUI needs. here is the link where I downloaded the libraries from: http://www.activestate.com/Products/ActiveTcl/ I?m not sure if this will help but, but it is well worth a try, as far as I think, because having the up-to-date TCL-libraries isn?t bad at all (even if they didn?t help you concerning the BioC-problem) cheers, Gregor Siegler Student TU Vienna Austria I am writing for a second time to ask for some help with a LimmaGUI error I am having. I am trying to load some BlueFuse results files into LimmaGUI. I am able to load the data in (seen in R window as being read in). I am using the other file type function in limmaGUI. I have no errors when reading the information in, and I am also able to create an M box plot with no normalization for all slides. The problem is that when I go to plot an M box plot with any combination of normalization (either within norm and/or between slide normalization) I get the following errors: Error: subscript out of bounds Then Error in assign ("MAwithinArrays", MA, limmaGUIenvironment) : Object MA not found. I am using R in Windows XP, version R 2.1.1 and LimmaGUI version 1.3.9 Please Help.... _________________________________________________________________ Die MSN Suche - Kategorien helfen Ihnen dabei, pr?zise Ergebnisse zu erhalten. http://search.msn.at/ Jetzt gratis downloaden!

Hi Jon, I couldn't tell you as I don't know how to command line operate limma.. If someone is prepared to help me I would love to learn, but I am finding it hard on my own.... Liz Message: 4 Date: Mon, 1 Aug 2005 19:18:29 -0400 From: jon butchar <butchar.2@osu.edu> Subject: Re: [BioC] LimmaGUI Error To: bioconductor at stat.math.ethz.ch Message-ID: <200508011918.29925.butchar.2 at osu.edu> Content-Type: text/plain; charset="iso-8859-1" Sorry that this probably isn't much help, but do you get the same errors when doing these plots via command line instead of the limma GUI? jon butchar