help on normalize only one species in two-species platform
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@zwanghivresearchorg-876
Last seen 10.2 years ago
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
Normalization genomes Normalization genomes • 993 views
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Ben Bolstad ★ 1.1k
@ben-bolstad-93
Last seen 10.2 years ago
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
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@lgautieralternorg-747
Last seen 10.2 years ago
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 >
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