[BioC] BlueFuse in limmaGUI [was LimmaGUI Error]

[Gordon Smyth]

>Date: Mon, 1 Aug 2005 15:29:51 -0500
>From: etbp2 at borcim.wustl.edu (Brooke-Powell, Elizabeth)
>Subject: [BioC] LimmaGUI Error
>To: <bioconductor at stat.math.ethz.ch>
>Cc: Gordon K Smyth <smyth at wehi.EDU.AU>
>
>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.

This isn't a complete specification of what you did. What column names did 
you specify (for both foreground and background)?

Since BlueFuse export files don't contain background intensities, have you 
tried setting the background correction method in limmaGUI to "none"?

Gordon

>  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