[BioC] Limma and limmaGUI with Imagene files, problems/bugs report

[Dr. Ir. B. van Breukelen]

Dear limma users and developers,

At our laboratory we analyze our MA data using limma. Currently we have
created a dedicated array on which the same set of genes is spotted three
times on one slide. Actually it is one design spotted three times. In
Imagene you can now create a META gid for (in this case) the 4*4 grids. This
grid you call grid A.. Then you can copy it several times (thereby creating
metagrid B and C). You then end up after quantification with a large imagene
file having the information of the three metagrids: (its like having three
slides on one slide!)
e.g.
Field	GridRow	GridCol	SpotRow	SpotCol	ID
A	1		1		1		1		Pp11
A	1		1		1		2		Pp12
..............
A	4		4		17		17		P..
B	1		1		1		1		Pp11
B	1		1		1		2		Pp12
..............
B	4		4		17		17		P..
C	1		1		1		1		Pp11
C	1		1		1		2		Pp12
..............
C	4		4		17		17		P..

When loading these files in either limma and limmaGUI only the A Field is 
read. Not the values belonging to the B and C metagrid (which are the
replicates). 
Is there a simple way to solve this problem ? Or do I have to cut these
files into three parts ?

Secondly, using limma and the targets <- readTargets function you cannot use
the targets object directly in the read.imagene function. I solved this
to create matrix with ncol=2 and nrow same as in the targets object. Then 
this can be used directly in read.imagene.
Next you would like to add color to your MA plots using controlTypes and
Spottypes. This doesn't work either because when reading the imagene data
files no columns RG$genes$Name and RG$genes$ID are created (actually onlu
RG$genes[['Gene ID']] exists.. I solved this by : RG$genes$Name <-
RG$genes[['Gene ID']] and same for ID. Then you will be able to use the
conrol types and colors for the colored MA plots. 
The same problem applies for limmaGUI. If you do not have a GAL file and
load the imagene files directly into limmaGUI you cannot assign colors using
spotTypes either. (Error messages appear already after loading the files).

I hope that the developers can implement these suggestions/workarounds for
these problems ?

Yours, Bas van Breukelen



=================================
Dr. Ir. B. van Breukelen
PostDoc, Bioinformatics, Molecular genetics
Dept. of Biology. 
Room N407: H.R. Kruytgebouw
Padualaan 8
3574 CH Utrecht

Tel:       +31(0)30 253 3355
Mobile: +31(0)6 24 996046
e-mail:  b.vanbreukelen at bio.uu.nl
website: http://genomics.bio.uu.nl/