[BioC] Converting data into MAlist to use in LIMMA

[Sean Davis]

On Wed, Feb 10, 2010 at 1:40 PM, Aubin-Horth Nadia
<Nadia.Aubin-Horth at bio.ulaval.ca> wrote:
> 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?

Hi, Nadia.

The limma package will work just fine with a matrix of log ratios.
You do not need to convert back to an MAList to use limma.

Sean