12.4 years ago by
Quoting Ziping Zhang <zipingcn at="" msu.edu="">:
> Dear Sir,
> I am using your limmaGUI for microarray analysis. My data is
> GenPix. limmaGUI was runing well last week. However, today it shows
> information when I was running a new set of data:
> limmaGUI was unable to read the image processing files listed in the
> 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
> Would you please kindly help me figure out how to solve the
> 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.
Dr. Jose I. de las Heras Email: J.delasHeras at
The Wellcome Trust Centre for Cell Biology Phone: +44 (0)131
Institute for Cell & Molecular Biology Fax: +44 (0)131
Swann Building, Mayfield Road
University of Edinburgh
Edinburgh EH9 3JR