J.delasHeras at ed.ac.uk
J.delasHeras at ed.ac.uk
Mon Apr 23 13:31:58 CEST 2007
Quoting solie.alizadeh at utoronto.ca:
> Dear all,
> I have a question about limmaGUI that is usually run in R environment.
> My problem is loading data into the programm. I have 6 gpr files that
> apparently are not compatible with limma. Everytime I'm trying to load
> the data (including a RNA targets file, an error appears:Error reading
> files. that I'm not sure,but seems to have something to do with the
> format of my files (gpr).
> Is that the problem? does anyone have any idea what it could be?
> I was wondering if I try GAL files, the problem would be solved. I
> still don't have access to the gal files that's why I haven't tried it
for questions about BioConductor packages (such as limma or limmaGUI)
you´re probably better off asking in the BioConductor forum. I
recommend you subscribe to it, it´s very much microarray-oriented and
I´ve learnt a lot there.
Now, about your question... I haven´t used limmaGUI for a long time (I
switched to teh command line limma instead, more flexible), but I´ve
dealt with similar problems as you describe, both my own and others...
I can´t tell you what you´re problem is, but I´ll give you a couple of
ideas so hopefully you can check and maybe one of them gives you a
Well, first of all, I´m concerned that you say you have no GAL file.
The GAL file describes what´s on the array, the locations of teh spots
etc... and limmaGUI *requires* a GAL file, as far as I remember... so
you won´t get far without one!
However, you say you gave GenePix files (GPR), so you could make your
own, as each GPR file will contain the minimal info that you need in a
GAL file: the columns with headers "block", "row", "column", "ID" and
The error reading the GPR files, was usually (when I encounter it) due
to non-standard headers in teh files. If you select "GenePix" as your
type of data file to load, by default it expects to find a column with
the header "F532 Median" and "F635 Median" as teh source of raw
intensity readings for the Cy3 and teh Cy5 channels respectively. But
depending on the settings of Genepix when teh scanning was made, and
when the quantitation was calculated, you may have a different
wavelength (maybe 685 instead of 635, etc)... so limmaGUI cannot find
teh right columns and returns an error. You should open all your GPR
files (in Excel, for instance... GPR is just a standard text file, in
tab-delimited format) and check what teh headers say. Take note of them.
If teh headers are not the same in all files, you´ll get errors.
To read GPR files with a different header than teh default, you can
simply use teh generic option ("Other", from teh menu of file
formats). This opens a little window where you specify teh actual
clñumn names to load from teh files. "Rf" means "Red Foreground"
(usually Cy5 channel), "Rb" is "Red backgrund", and similarly you get
to specify teh column names for "Gf" and "Gb". So, say you could write
"F650 Median" in the "Rf" slot, and this tells limmaGUI to take that
column you specified as teh source for the signals for teh Cy5
channel. "B650 Median" on the slot "Rb" then specifies that column
from the GPR files as teh background for Cy5 channel... etc.
I´d say the reason above is the most likely to solve the problem.
However, I have also seen instances where some GPR files had been
modified to omit any empty spots, for example. This results in having
files containing different numbers of genes, and this returns errors.
So make sure all teh files have teh right number of rows, and that the
GAL file has teh same number of rows too, and in the same order!
I hope this helps a bit... and do check the BioConductor forum, it is
a great place to ask this sort of questions, especially as you are
more likely to get answers directly from teh guys who developed the
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
Swann Building, Mayfield Road
University of Edinburgh
Edinburgh EH9 3JR
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