[BioC] BlueFuse in limmaGUI [was LimmaGUI Error]

[Gordon Smyth]

At 01:41 AM 3/08/2005, Brooke-Powell, Elizabeth wrote:
>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

How exactly have you told it not to background correct? The exact sequence 
of reading in and dialog boxes.

>  as it cannot with non
>GenePix, Spot etc files.

Yes it can, with any program that gives background estimates, i.e., 
anything other than BlueFuse.

>  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.

Are you saying that the analysis that you are doing works in a previous 
version of limmaGUI, but not in the version you are using?

Gordon

>  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