Hi Ali, > Hi Ali, > > On 10/20/2011 2:49 AM, Ali Mo [guest] wrote: >> Hi every one. >> >> I am using 384 well qPCR array for miRNA study. I wanted to normalize my >> results using affy. How can I create an affybatch wich contains my Cq >> values? Thanks a lot. > > You don't want to do this. Trying to stuff qPCR data into an AffyBatch > is asking for trouble. Quantile normalizing qPCR data is asking for > trouble as well, IMO, but they are your data. > In case you want to try some other normalisation methods, including e.g. geometric mean which has been recommended for miRNA data, then you might want to have a look at the HTqPCR package. If you type library(HTqPCR) vignette("HTqPCR") that should give you enough instructions on how to start, if you're not too familiar with Bioconductor. There's also a brief comparison of 4-5 different normalisaiton methods, including quantile. HTH \Heidi > If you want to quantile normalize these data, use normalizeQuantiles() > from the limma package. > > Best. > > Jim > > >> >> PS. I am new to R/bioconductor. >> >> -- output of sessionInfo(): >> >> No R command! >> >> -- >> Sent via the guest posting facility at bioconductor.org. >> >> _______________________________________________ >> 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 > > -- > James W. MacDonald, M.S. > Biostatistician > Douglas Lab > University of Michigan > Department of Human Genetics > 5912 Buhl > 1241 E. Catherine St. > Ann Arbor MI 48109-5618 > 734-615-7826 > > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should not > be used for urgent or sensitive issues > > _______________________________________________ > 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 >