Hi, I would like first say thanks to Gordon and Stephen for replying my last question. I have a need to normalize each genes in my samples to a particular control sample. Is there a package or function in Bioconductor can perform this kind of actions? I appreciate if someone could inform me on this issue. Leon [[alternative HTML version deleted]]

Leon, I don't follow exactly what you want to do. If I don't understand it, probably others on the list don't either. You might explain more fully what you have in mind. Best wishes Gordon At 07:26 AM 20/06/2003, leon ding wrote: >Hi, > >I would like first say thanks to Gordon and Stephen for replying my last >question. >I have a need to normalize each genes in my samples to a particular >control sample. >Is there a package or function in Bioconductor can perform this kind of >actions? I appreciate if someone could inform me on this issue. > >Leon > > [[alternative HTML version deleted]] > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor

It sounds as if you simply want to estimate differential expression between your sample RNA and your control RNA. (I am guessing that all your arrays include some common reference RNA, although you don't say this.) If this is what you want to do, then Section 6 "Two-Sample Experiments" of the LIMMA User's Guide gives a detailed example of how to go about it. Gordon At 11:01 AM 20/06/2003, leon ding wrote: >Hi, Gordon. > >Thanks for your prompt response. >What I want to do is to somehow divide log ratios (M-values) in each >replicate slide by log ratios in a control slide (or average M from >replicate control slide) on a per gene basis. In another word, >[M_gene1_sample / M_gene1_control]. The ideal way is that I could do this >after NormalizeWithinArrays and then do lm.series and ebayes. I hope I >coould find a solution within limma. > >Leon > > >Gordon Smyth <smyth@wehi.edu.au> wrote: >Leon, > >I don't follow exactly what you want to do. If I don't understand it, >probably others on the list don't either. You might explain more fully what >you have in mind. > >Best wishes >Gordon > >At 07:26 AM 20/06/2003, leon ding wrote: > >Hi, > > > >I would like first say thanks to Gordon and Stephen for replying my last > >question. > >I have a need to normalize each genes in my samples to a particular > >control sample. > >Is there a package or function in Bioconductor can perform this kind of > >actions? I appreciate if someone could inform me on this issue. > > > >Leon > > > > [[alternative HTML version deleted]] > > > >_______________________________________________ > >Bioconductor mailing list > >Bioconductor@stat.math.ethz.ch > >https://www.stat.math.ethz.ch/mailman/listinfo/bioconducto! r