Dear Jay, Assuming x is the annotatedPeak as a data frame, and y is the peak with fold information, you can do z = merge(x, y). Please make sure x and y have common column names for merging. If not, you will need to specify the column names with by.x and by.y in merge. For more information about merge, please type help(merge) in R. Best regards, Julie On 9/5/12 5:58 PM, "Wang, Jianhui" <jianhui.wang@yale.edu> wrote: Hi dear Julie, I'm using chippeaksanno. It works perfectly. Could you tell me how to dump out the enrichment fold information in the input after I finish the TSS analysis? I found that the enrichment fold lost when I used write.table(as.data.frame(annotatedPeak), file="annotatedPeakList.xls", sep="\t", row.names=FALSE). Thank you. Jay [[alternative HTML version deleted]]