Dear Bioconductors, I like to analyze Agilent one color Microarrays and need some input. Which normalization method would be the best for mRNA and which for miRNA. Agilent couldn’t get me a god support, because they have a specific for analyzing data. Thank you very much for your help! Best, Anke [[alternative HTML version deleted]]

Dear Anke, since I haven't seen a response to your post yet: I don't think there is "the best" normalization method for either mRNA or miRNA but your choice will rather depend on your data and assumptions... but have a look at the BioC packages Agi4x44PreProcess and AgiMicroRna and their vignettes; they will let you try and compare some methods easily. (Personally, I most often use vsn for mRNA and RMA for miRNA.) Cheers, - axel Axel Klenk Research Informatician Actelion Pharmaceuticals Ltd / Gewerbestrasse 16 / CH-4123 Allschwil / Switzerland From: Anke Wendschlag <anke.wendschlag at="" googlemail.com=""> To: bioconductor at r-project.org Date: 16.04.2011 12:29 Subject: [BioC] advise normalization for Agilent one color Microarray for mRNA and miRNA Sent by: bioconductor-bounces at r-project.org Dear Bioconductors, I like to analyze Agilent one color Microarrays and need some input. Which normalization method would be the best for mRNA and which for miRNA. Agilent couldn?t get me a god support, because they have a specific for analyzing data. Thank you very much for your help! Best, Anke [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor at r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor The information of this email and in any file transmitted with it is strictly confidential and may be legally privileged. It is intended solely for the addressee. If you are not the intended recipient, any copying, distribution or any other use of this email is prohibited and may be unlawful. In such case, you should please notify the sender immediately and destroy this email. The content of this email is not legally binding unless confirmed by letter. Any views expressed in this message are those of the individual sender, except where the message states otherwise and the sender is authorised to state them to be the views of the sender's company. For further information about Actelion please see our website at http://www.actelion.com