[BioC] help for limmaGUI

[J.delasHeras at ed.ac.uk]

Quoting Ziping Zhang <zipingcn at msu.edu>:

> Dear Sir,
>
> I am using your limmaGUI for microarray analysis. My data is collected by
> GenPix. limmaGUI was runing well last week. However, today it shows me these
> information when I was running a new set of data:
>
> limmaGUI was unable to read the image processing files listed in the Target
> files
> Error in assign(“RG”,RG,limmaGUIenvironment):object”RG” not found
> Error in MA.RG(RG):Object doesn’t contain R and G components
> Error in assign(“MAraw”,MAraw, limmaGUIenvironment): object “MAraw”
> not found
> Error in assign(“MA”, MAraw, limmaGUIenvironment): object”MAraw” not
> found
>
> Would you please kindly help me figure out how to solve the probelem. Thanks
> a lot.
>
> Zhang, Ziping (Ph.D.)
> Department of Fisheries and Wildlife
> 13 Natural Resources Building
> 158 Giltner Hall
> Michigan State University
> East Lansing, MI 48824
> Tel: 517-4323314
> Fax: 517-4321699

I think the key is that it is a *new* data set.
Check the files (GPR files are just tab-delimited text files) and make  
sure that the names of the columns are what LimmaGUI expects. I'm only  
talking about the foreground and background columns (something like  
"F635 Median" and "B635 Median" etc), there are many other columns  
that are ignored by LimmaGUI. Chances are that some of those columns  
have a slightly different name, for instance, "F635 Median" may appear  
as "F685 Median", depending on how teh scanning options were set up...
Once you identify the problem, you can just change the column name  
manually, or use the "Other" option when you're asked to read the  
files, rather than GenePix, and specify explicitly the names of the  
columns to be read.
Just be sure that ALL your files have the same column names, as you  
only need one mismatch to get errors.

Good luck!

Jose

-- 
Dr. Jose I. de las Heras                      Email: J.delasHeras at ed.ac.uk
The Wellcome Trust Centre for Cell Biology    Phone: +44 (0)131 6513374
Institute for Cell & Molecular Biology        Fax:   +44 (0)131 6507360
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University of Edinburgh
Edinburgh EH9 3JR
UK