How to read a data.frame into limma or marray
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@wolfgang-raffelsberger-1805
Last seen 8.4 years ago
Dear list, the question might seem trivial, I just couldn't find a function to transform a simple data.frame with microarray log2-ratios into a limma-type ot marray-type objects. I have a data.frame containing (R/G-) log2-ratios for the each slide in a separate column and I 'd like to use some of the functions available in limma or marray, in particular to run a lowess normalization. I realized that I need either limma or marray specific (S4-) objects but I couldn't find a function for easily creating one of these. I guess I'll need either a class 'marrayNorm' object or an 'MAList', but I couldn't find a specific function to do so. Or is it necessary to create an exprSet first, to be able to transform the data the to an MAList ? Any suggestions ? Just for clarification : I run R-2.6.0 with BioC 2.1 Thank's in advance, Wolfgang . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Wolfgang Raffelsberger, PhD Laboratoire de BioInformatique et G?nomique Int?gratives CNRS UMR7104, IGBMC 1 rue Laurent Fries, 67404 Illkirch Strasbourg, France Tel (+33) 388 65 3300 Fax (+33) 388 65 3276 wolfgang.raffelsberger at igbmc.u-strasbg.fr
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@saroj-mohapatra-1446
Last seen 8.4 years ago
Hi Wolfgang: If your matrix is called M (and there is another matrix called A), then the following would create an MAList object. > MA <- new("MAList",list(M=M,A=A)) For example: --------------------------------------------------------------------- > library(limma) > my.df=as.data.frame(matrix(rnorm(8000), ncol=4, nrow=2000)) > colnames(my.df)=paste("M.", 1:4, sep="") > rownames(my.df)=paste("probe.", 1:2000, sep="") > M=my.df > A=my.df > MA <- new("MAList",list(M=M,A=A)) > MA[1,] An object of class "MAList" $M M.1 M.2 M.3 M.4 probe.1 0.02481883 0.3764408 -0.1547271 -0.362104$A M.1 M.2 M.3 M.4 probe.1 0.02481883 0.3764408 -0.1547271 -0.362104 --------------------------------------------------------------------- Best, Saroj Wolfgang Raffelsberger wrote: >Dear list, > >the question might seem trivial, I just couldn't find a function to >transform a simple data.frame with microarray log2-ratios into a >limma-type ot marray-type objects. >I have a data.frame containing (R/G-) log2-ratios for the each slide in >a separate column and I 'd like to use some of the functions available >in limma or marray, in particular to run a lowess normalization. I >realized that I need either limma or marray specific (S4-) objects but I >couldn't find a function for easily creating one of these. I guess I'll >need either a class 'marrayNorm' object or an 'MAList', but I >couldn't find a specific function to do so. >Or is it necessary to create an exprSet first, to be able to transform >the data the to an MAList ? >Any suggestions ? > >Just for clarification : I run R-2.6.0 with BioC 2.1 > >Thank's in advance, >Wolfgang > > >. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . > >Wolfgang Raffelsberger, PhD >Laboratoire de BioInformatique et G?nomique Int?gratives >CNRS UMR7104, IGBMC >1 rue Laurent Fries, 67404 Illkirch Strasbourg, France >Tel (+33) 388 65 3300 Fax (+33) 388 65 3276 >wolfgang.raffelsberger at igbmc.u-strasbg.fr > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > >