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Hi Sharon, Sharon wrote: > Hi, > > I am analysing 'rgu34a' affy chips. > I was able to extract expression values using 'rma' and > store the expression values in > the 'txt' file. When, I tired to read the 'txt' file using read.table(), > I get NA values (for all chips. but in the txt file, i do see the expression > values) for probesets such as D37951UTR#1_at. I tried to use > check.names=FALSE and as.is=TRUE options but not able to solve the issue. > > Any suggestions? My suggestion would be to not write the expression values to a text file. One of the goals of the Bioconductor project is to create and use data structures (such as the exprSet that originally contained your data) that can be used by all of the packages, and that are designed to contain all the information needed to track and describe the data. By writing the data to a text file and then reading it back in, you are adding two completely unneccessary steps to your analysis. In addition, you are replacing something specific and more useful (an exprSet) with something general and arguably much less useful (a data.frame). Best, Jim > > Thanks in advance. > > regards, > sharon > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.

Hi, try setting the argument comment.char as by default is set to "#", for example: read.table("filename", comment.char="") HTH, D. On Wed, 27 Sep 2006, Sharon wrote: > Hi, > > I am analysing 'rgu34a' affy chips. > I was able to extract expression values using 'rma' and > store the expression values in > the 'txt' file. When, I tired to read the 'txt' file using read.table(), > I get NA values (for all chips. but in the txt file, i do see the expression > values) for probesets such as D37951UTR#1_at. I tried to use > check.names=FALSE and as.is=TRUE options but not able to solve the issue. > > Any suggestions? > > Thanks in advance. > > regards, > sharon > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 >