Thanks for the help I fixed it the problem was that I was not selecting the right column at all! how silly of me so this fixes it: p<-Data[,c('pval')] p.adj <- p.adjust(p, method = "fdr", n= length(p)) write.table(p.adj, file="filename", sep="\t") I am using multtest now in any case thanks again Lucia On Fri, Jan 7, 2011 at 3:55 PM, Martin Morgan <mtmorgan@fhcrc.org> wrote: > On 01/07/2011 11:52 AM, Lucia Peixoto wrote: > > Hi > > > > I was having some issues with the p-values of differential expression of > my > > samples using SAM, so I to compare with more traditional multiple testing > > approaches > > I thought I will just do a ttest and then use p.adjust to get BH > corrected > > pvalues > > My input is just a two column textfile where the first column is the Affy > > probe IDs and the second is the ttest pvalue > > All I get out is the same p-values I put in, since I am a pretty naive R > > programmer I am sure there is something simple I am doing wrong > > > > help will be greatly appreciated, thanks!! > > > > here is my script: > > > > Data<-read.table("input", header=TRUE, row.names=1) > > p.adj <- p.adjust(Data, method = "BH", n= length (Data)) > > Hi Lucia -- > > > df = data.frame(x=1:5) > > dim(df) > [1] 5 1 > > length(df) > [1] 1 > > A data frame is treated as a list of columns, so length(df) is the > number of columns; you probably want nrow(Data) (or nothing, and > p.adjust will do the right thing). > > Martin > > > > write.table(p.adj, file="output", sep="\t") > > > > My output is identical to my input > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > -- > Computational Biology > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 > > Location: M1-B861 > Telephone: 206 667-2793 > [[alternative HTML version deleted]]