[BioC] Loading multiple Affy chips simultaneously

[Paul Boutros]

Hello,

I'm trying to analyze & merge some rat data that was generated on two
separate Affymetrix chips (RAE230-A and RAE230-2).  One chip (RAE230-2) is a
superset of the other.  Approximately equal numbers of animals were analyzed
with the smaller array (n=9) as the larger (n=10).  

I would like to:
a) pre-process (via GC-RMA) the two datasets separately
b) subset the summarized expression levels of the larger chip
c) merge the subsetted dataset with the smaller one
d) perform statistical analysis on the overall data (e.g. with limma)

My code loads the data like this:
data.batch1 <- ReadAffy(filenames=cel.files.batch1,
phenoData="phenodata_batch1.txt");
data.batch2 <- ReadAffy(filenames=cel.files.batch2,
phenoData="phenodata_batch2.txt");

Then does some diagnostics such as:
par( mfrow = c(1,2) );
hist(data.batch1, main = "Batch 1");
hist(data.batch2, main = "Batch 2");

Which generates the warnings:
Attaching package: 'rat2302cdf'

        The following object(s) are masked from package:rae230acdf :
         i2xy 

        The following object(s) are masked from package:rae230acdf :
         xy2i

I was not sure if this is a problem or not.  I later go on to use the
functions AffyRNAdeg and gcrma, and I am wondering if this masking will
interfere with their correct operation?  In other words, do I need to
process the two batches sequentially, or can I do it in parallel as I've
shown here?

Many thanks for any help,
Paul