Hi Eric, You have NA in your name column. One fix for you without creating a name column is to just use the following code to create RangedData from your dataframe. RangedData(Iranges(start=as.numeric(as.character(TwoLplus[,2])), end=as.numeric( as.character(TwoLplus[,3])),names=paste(TwoLplus[,1], TwoLplus[,2], TwoLplus[,3])), space= as.character(TwoLplus[,1]), strand= as.character(TwoLplus[,6])) Best regards, Julie ******************************************* Lihua Julie Zhu, Ph.D Research Associate Professor Program Gene Function and Expression University of Massachusetts Medical School 364 Plantation Street, Room 613 Worcester, MA 01605 508-856-5256 http://www.umassmed.edu/pgfe/faculty/zhu.cfm On 2/26/10 3:20 PM, "Eric Bremer" <ericgbremer@gmail.com> wrote: > Hi Julie, > Thanks so much for your help so far.  I have been trying to convert some of my > data from a BED format into the ranged data and seem to run into a couple of > errors that I can not seem to fix.  Here is an example: > >> > TwoLplus = read.table("2Lplus_bed2.txt", header=TRUE, sep="\t", fill=TRUE) >> > test = BED2RangedData(TwoLplus, header=TRUE) > Error in `rownames<-`(`*tmp*`, value = c(NA_character_, NA_character_,  : >   missing values not allowed in rownames > In addition: Warning messages: > 1: In `[<-.factor`(`*tmp*`, strand == "+", value = 1) : >   invalid factor level, NAs generated > 2: In `[<-.factor`(`*tmp*`, strand == "-", value = -1) : >   invalid factor level, NAs generated >> > head(TwoLplus) >   chrom peakStart peakEnd name score strand > 1 chr2L      9115    9140   NA    NA      + > 2 chr2L      9410    9489   NA    NA      + > 3 chr2L     12342   12368   NA    NA      + > 4 chr2L     25256   25281   NA    NA      + > 5 chr2L     27909   27934   NA    NA      + > 6 chr2L     30731   30756   NA    NA      + >> > > > > I have also attached the origninal .txt file that I am starting with.  I > suspect that I am missing something simple (at least I hope so) > Thanks! > Eric [[alternative HTML version deleted]]