Hi Paul, This error message shows up because the R session needs to load an package for each chip. The package included two function i2xy and xy2i, which can convert probe coordinate to an integer and vice versa. Because you are using two chips in one session. When the second package is loaded, its two functions i2xy and xy2i would mask the first package's functions. This doesn't affect rma according to my experience, because rma doesn't use these two functions at all. I am not sure about GCRMA. Actually a better solution for your problem is to use a tool we developed, which can split RAE230-2 celfile to a pair of RAE230-A and RAE230-B celfiles. All the hassles you met now would be gone. The tool is http://arrayanalysis.mbni.med.umich.edu/MBNIUM.html#MBNIUM Just let me know if you came across any problem. Best, Manhong > Date: Sat, 27 Jan 2007 13:58:56 -0500 > From: "Paul Boutros" <paul.boutros at="" utoronto.ca=""> > Subject: [BioC] Loading multiple Affy chips simultaneously > To: <bioconductor at="" stat.math.ethz.ch=""> > Message-ID: <000001c74245$328370c0$ec02a8c0 at main> > Content-Type: text/plain; charset="us-ascii" > > 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