[BioC] GEOquery doubt: converting GDS into a MAlist

[Juan C Oliveros Collazos]

Hi all,

I am trying to dowload a set of data samples from GEO database by using 
GEOquery package:

Example:
-------------------------------

library (GEOquery);

gds <- getGEO("GDS1047");

gpl<-getGEO("GPL198");

MA <- GDS2MA(gds, GPL = gpl);
--------------------------------

By the GEOquery user manual, this result in a MAlist containing all 
details about the experiment.

As far as I understand, the MAlist object is used for storing M values 
and A values, amongst other details.

* M values are defined as the logRatio of all genes in each comparison.

* A values are defined as the average of logIntensities for each comparison.

However, the MAlist created with GDS2MA seems not to store in "M" the 
logRatios but only the intensities corresponding to every GSM in the 
dataset.


I need to use the logRatios (M) of a lot of experiments and I would 
write an script that automatically download and store these M values in 
tables.

Obviously, the script should be able to deduce which comparisons are 
involved in the dataset (which GSM are numerators and which are 
denominators)

Now I can store the intensities of the GSMs, but to convert these 
intensities in ratios I need to check which are the comparisons by 
hand... I would like to avoid this.

Any help?

Thanks in advance!

Best,

Juan Carlos



-- 
Juan Carlos Oliveros
BioinfoGP, CNB-CSIC

** NEW EMAIL ADDRESS: oliveros at cnb.csic.es **