[BioC] Converting data into MAlist to use in LIMMA

[Aubin-Horth Nadia]

HI everybody

We conducted a two-color microarray experiment using a 19 000-probe  
home made cDNA array. Our experiment contains 12 arrays. We use LIMMA  
to do all the normalization and model fitting and stats. Out of the 19  
000 probes, several clones are part of the same contig, as annotated  
by TIGR. We decided to average the M values for these clones that  
correspond to a single contig to obtain a single M value for a given  
contig, for each array separately. We also wanted to remove probes  
that were called empty after sequencing (but they were already on the  
printed microarray). We exported the MAlist containing the normalised  
data (called "MAptip.nba.scale") and extracted the M data for each of  
the 12 slides in Python. We did the averaging and removing of "empty"  
spots and now have a new file with columns containing information on  
block, row, column, spot ID, annotation information for the contigs  
(and singletons) and then data for each slide in the following  
columns. Each row contains the averaged M values.

We looked for a way to convert this file back into a MAlist so we can  
specify our design and do a fit. We read in the archives about a  
library called convert (which we did not find on CRAN) and info on how  
to transform data into an exprSet for affy data. Would someone be  
willing to help us with this task and give us pointers?

Thank you very much

Nadia Aubin-Horth
Assistant professor
Biology Department
Institute of Integrative and Systems Biology
Université Laval
Québec, Canada