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Hi, Karen, You can choose type "affinities" in bg.adjust.gcrma. You will also need to specify which probes you would consider as negative controls ("NCprobes") in order to estimate the relationship between background and probe sequences. If, in your experiment, only a small fraction of probes are expected to have specific target (for example, only a small fraction of genes are expressed), you can use all PM probes as NCprobes if there's no other choice. bg.adjust.gcrma(object, NCprobe= index.of.your.control.probes,type="affinities") Is the hybridization method the same as what's used for standard GeneChip arrays? If not, you may want to estimate the object "affinity.info" using your own data instead of the default. In this case you will either need negative control probes or run an negative control experiment. Jean Wu On Wed, 25 Oct 2006, Karen Vranizan wrote: > I have a PM-only Affy chip. Is it possible to do gcrma on this data? Thank you. > > Karen Vranizan > Functional Genomics Lab > 261A Life Sciences Addition > Mail Code #3200 > UC Berkeley, CA 94720-3200 > > Phone: 510-642-7520 > Fax: 510-643-2685 > email: vranizan at berkeley.edu > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >