Hi I am using bioconductor and limma for analysing some cDNA moicroarray data, I would like to export the normalized MA data ( normalized cy3 anb cy5 values) as tab delimited text file...Could you please tell how I could do that ? Seby Edassery Bioinformatics Specialist/Programmer University of Illinois at Chicago Research Resources Center -Core Genomics, 835 South Wolcott Avenue, Rm A302 (mc937) Chicago, IL 60612-7341 Phone 312 413 9290 Fax 312 996 0539 Webpage - http://www.uic.edu/depts/rrc/cgf/ [[alternative HTML version deleted]]

Assuming your data are in an MAlist (called say, my.malist), you should be able to do something like write.table(my.malist$M, "M values.txt", sep="\t", quote=FALSE, col.names=NA) write.table(my.malist$A, "A values.txt", sep="\t", quote=FALSE, col.names=NA) Note that these are _not_ the normalized cy3 and cy5 data, but the M and A values. You will have to convert back to normalized intensity values if that is what you want. HTH, Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> Seby <edassery@uic.edu> 04/07/04 03:02PM >>> Hi I am using bioconductor and limma for analysing some cDNA moicroarray data, I would like to export the normalized MA data ( normalized cy3 anb cy5 values) as tab delimited text file...Could you please tell how I could do that ? Seby Edassery Bioinformatics Specialist/Programmer University of Illinois at Chicago Research Resources Center -Core Genomics, 835 South Wolcott Avenue, Rm A302 (mc937) Chicago, IL 60612-7341 Phone 312 413 9290 Fax 312 996 0539 Webpage - http://www.uic.edu/depts/rrc/cgf/ [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor

Seby, If you actually want the normalised R and G intensity values rather than the MA values there is a simple function in limma to convert your normalised MA list to a RG list. >RGnorm <- RG.MA(MA) >write.table(RGnorm$R, file="Rvalues.txt") >write.table(RGnorm$G, file="Gvalues.txt") Regards, Matt