[BioC] LimmaGUI and limma

[James Wettenhall]

Hi Binita,

On Tue, 31 Aug 2004, Binita Dutta wrote:
> I want to analyse my data in limmaGUI. We have our own chip and use agilent
> scanner to scan the  slide. Later the scanned image is analysed by "Array
> vision" program. We export the data from Array vision as text file and then
> upload the text file in the database.

limmaGUI should be able to read in ArrayVision files OK.  Just
follow the "Swirl" example in the documentation, replacing the
SPOT files (listed in the Targets file) with ArrayVision files.

> (It is possible to export the files from our database as text file).

limmaGUI is not designed to interact directly with a database.
You should use standard ArrayVision files (in tab-delimited text
format), so if this requires exporting from your database, then
do that, (but ensure that importing/exporting files into/out of
database hasn't modified them from their original ArrayVision
format).

> With this set up, I want to know how I can analyse the data with limmaGUI.

This question is too general.  Please say whether you have
attempted to read the limmaGUI documentation and run through
examples, and where you have succeeded/failed using the example
data set(s) e.g. Swirl, and whether you have succeeded/failed
in reading in your own data into limmaGUI.

> One more question: can I import normalised M and A values from other
> program and then perform linear model fit using limma.

Yes, certainly, but limma has plenty of good normalisation
methods for two-colour arrays, so you might not need to.  There
is a feature in limmaGUI designed to input M and A values
obtained from output from the former marrayTools (now part of
marray).  So if you can get your normalised  M A data in this
format, then you can use this feature.  But it is easier to do
the normalisation in limma/limmaGUI, unless you have a specific
reason why you want to do normalisation elsewhere.

Regards,
James