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