Hi Petr, Thank you. Yes, normalized.matrix" and "normalized" are the same, my mistakes.
Operators: like Cyclic loess normalization and quantile Normalization, from limma or affy packages. Would cv= sd/mean be a better replacement for sd? On 4/5/12, Petr Savicky [via R] <ml-node+s789695n4535407...@n4.nabble.com> wrote: > > > On Thu, Apr 05, 2012 at 07:46:52AM -0700, ali_protocol wrote: >> Hi all, >> >> I have a matrix (n*2), I want to compare 2 operators (2 normalization for >> array results) on these matrix. >> The 2 columns should ideally become the same after operations >> (normalization). So to compare operations, >> I do this for each normalization: >> >> s= sum (apply (normalized.matrix, 2,sd)) >> c= cor (normalized[,1],normalized [,2], method='pearson') >> >> >> I expect that if normalization 1 is superior, s should be less and c >> greater >> than normalization2, but both s and c change in 1 direstion. Is this >> possible or am I doing something wrong? > > Hi. > > Is "normalized.matrix" and "normalized" the same matrix? > > Can you specify, which operators you use for normalization? > > Without having this information, i guess that comparing the > correlations alone can be used, since it does not depend on > the scaling the numbers. By an appropriate scaling factor, > the sd may be changed to any value, but this does not say > much about the amount of information in the data. On the other > hand, the correlation does not change by scaling, so it may > be a more reliable measure. > > Note that > > apply(normalized.matrix, 2, sd) > > is the same as > > sd(normalized.matrix) > > Hope this helps. > > Petr Savicky. > > ______________________________________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > > > _______________________________________________ > If you reply to this email, your message will be added to the discussion > below: > http://r.789695.n4.nabble.com/Sum-of-sd-between-matrix-cols-vs-spearman-correlation-between-them-tp4535057p4535407.html > > To unsubscribe from Sum of sd between matrix cols vs spearman correlation > between them, visit > http://r.789695.n4.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_code&node=4535057&code=bW9oYW1tYWRpYW5hbGltb2hhbW1hZGlhbkBnbWFpbC5jb218NDUzNTA1N3wtMTkwNDgxNTk3NQ== -- View this message in context: http://r.789695.n4.nabble.com/Sum-of-sd-between-matrix-cols-vs-spearman-correlation-between-them-tp4535057p4538971.html Sent from the R help mailing list archive at Nabble.com. [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
