[BioC] BlueFuse in limmaGUI [was LimmaGUI Error]

[Brooke-Powell, Elizabeth]

Thank you all for you responses. I am sorry I didn't give enough
information. 

I have done what I have always done with BlueFuse, I have told LimmaGUI not
to use background correction or spot quality calls as it cannot with non
GenePix, Spot etc files. When using the other file type function I set the
foreground and background to be the same header (so the Cy5 foreground and
background are AMPCH2 and cy3 is AMPCH1). If I don't use a header it
recognizes it won't load.  This has never been a problem in the past as I
tell it to ignore background. The problem doesn't seem to be in the file
loading, but rather in the M box plot generation with normalization.
LimmaGUI is taking in all the data, targets file and spot types, and can
generate a an M box plot without normalization. I loaded some ScanArray
files in the same way and that worked just fine including the normalization.
I am beginning to believe that the problem is when I use BlueFuse Fused data
out put files... I am just not sure why.... 

Hope that adds some more information...

Liz

-----Original Message-----
From: Gordon Smyth [mailto:smyth at wehi.edu.au] 
Sent: Tuesday, August 02, 2005 5:27 AM
To: Brooke-Powell, Elizabeth
Cc: bioconductor at stat.math.ethz.ch
Subject: [BioC] BlueFuse in limmaGUI [was LimmaGUI Error]


>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