Hi All, Can anyone instruct me how to do RMA normalization for Plasmodium/Anopheles platform, which contains both malaria parasite and mosquito genomes, when my mRNA samples were from Plasmodium only. In other words, how can I mask Anopheles genome when I do RMA normalization. Thanks Zhining

I don't know how probesets are structured on such chips, but if they are distinct species specific probesets you should be able use the subset parameter for the rma() function. Ben On Thu, 2004-08-05 at 12:36, zwang@hivresearch.org wrote: > Hi All, > > Can anyone instruct me how to do RMA normalization for > Plasmodium/Anopheles platform, which contains both malaria parasite and > mosquito genomes, when my mRNA samples were from Plasmodium only. In other > words, how can I mask Anopheles genome when I do RMA normalization. Thanks > > > Zhining > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- Ben Bolstad <bolstad@stat.berkeley.edu> http://www.stat.berkeley.edu/~bolstad

zwang@hivresearch.org wrote: > Hi All, > > Can anyone instruct me how to do RMA normalization for > Plasmodium/Anopheles platform, which contains both malaria parasite and > mosquito genomes, when my mRNA samples were from Plasmodium only. In other > words, how can I mask Anopheles genome when I do RMA normalization. Thanks Use a specific cdfenv. The pack 'altcdfenvs' can help you. See: http://www.bioconductor.org/repository/devel/vignette/ngenomeschips.pd f L. > > Zhining > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >