[BioC] Quantile Normalization on mice data

[Yen Lin Chia]

Hi,

I'm working on some mice data from two batches (experiment carried out
different time), but what I'm interested is to compare the gene
expression between two stages

Stage I:  2 mice from batch D and 1 mouse from batch E
Stage II: 1 from batch D and 4 from batch E.

Two tissue samples are taken for each mouse, center of the tumor and the
rim of the tumor.  Thus, I have two set of results layout
(above-mentioned).  My first thought is to normalize the rim and core of
the tumor separately, but ignoring the batch variation.  Wonder if this
is a good apprach.

Will the batch variation be problematic, from box plots, you can group
the plots into batches (regardless of stages).

I'm trying to estimate the batch effect by using affyPLM, (i.e. dropping
samples as a factor), is p-values computed along with the function?  I
only see the estimates and standard error.  I'm new to R and
bioconductor packages.

Thanks.

Yen Lin