Hi Yen Lin, I've read your posting from 11 Feb to the BioC list about the design of your experiment with two "batches" of mice. I've a similar experimental layout: mouse cell cultures treated with a drig at different doses. The experiment was carried out three times under the same experimental conditions but in different laboratories. >From a hierachcical clustering and a principle component analysis of the cross-chip normalized probe sets I can clearly see that the batches cluster together. I've used affyPLM to shed some light into the experiment, however, I'm a bit lost with the interpretation. I was wondering how in the end you analysed your data. Did you try to use your own full factorial model for fitPLM, e.g. in your case PM ~ -1 + probe + stage + batch I've tried this with my experiment but I'm not sure how to interpret the output ... . kind regards, Arne > -----Original Message----- > From: bioconductor-bounces@stat.math.ethz.ch > [mailto:bioconductor-bounces@stat.math.ethz.ch]On Behalf Of > Yen Lin Chia > Sent: 11 February 2004 07:09 > To: bioconductor@stat.math.ethz.ch > Subject: [BioC] Quantile Normalization on mice data > > > 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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >