Version:1.0 StartHTML:0000000149 EndHTML:0000001752 StartFragment:0000000199 EndFragment:0000001718 StartSelection:0000000199 EndSelection:0000001718 I am trying to use a large dataset for ChIPpeakAnno analysis. A sample of my bed file looks like name chromStart chromEnd strand chrom 1 NM_001001398 13196926 13203469 -1 chr25 2 NM_001001399 4025604 4033166 -1 chr19 3 NM_001001401 12007237 12036869 1 chr14 4 NM_001001402 8387701 8401691 1 chr22 5 NM_001001403 6729898 6782124 -1 chr3 6 NM_001001406 39498223 39506396 1 chr19 7 NM_001001407 3585650 3602600 -1 chr15 8 NM_001001409 38023452 38029815 1 chr20 9 NM_001001501 3187183 3217911 -1 chr6 When I use BED2RangedData I get this error: test.rangedData = BED2RangedData(test.bed) Error in `rownames<-`(`*tmp*`, value = c("-1", "-1", "1", "1", "-1", "1", : duplicate rownames not allowed In addition: Warning message: In BED2RangedData(test.bed) : NAs introduced by coercion Why is this? Abi [[alternative HTML version deleted]]

Hi Abirami, Your file is not in bed file format. Please check out the bed file format definition at http://genome.ucsc.edu/FAQ/FAQformat.html#format1. The orders of the columns are important. In addition, currently BED2RangedData uses the name column as rownames of the RangedData which needs to be unique. If the name column is missing, BED2RangedData will assign rownames automatically. Here is an example. test.bed = data.frame(cbind(chrom = c("1", "2"), chromStart=c("100", "1000"),chromEnd=c("200", "1100"), name=c("peak1", "peak2"))) test.rangedData = BED2RangedData(test.bed) Please type ?BED2RangedData in a R session for more details. BTW, it would be helpful to include the session information for future correspondence. 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 4/20/10 3:48 PM, "Abirami Subbu" <abi.bio.86@gmail.com> wrote: name chromStart chromEnd strand chrom 1 NM_001001398 13196926 13203469 -1 chr25 2 NM_001001399 4025604 4033166 -1 chr19 3 NM_001001401 12007237 12036869 1 chr14 4 NM_001001402 8387701 8401691 1 chr22 5 NM_001001403 6729898 6782124 -1 chr3 6 NM_001001406 39498223 39506396 1 chr19 7 NM_001001407 3585650 3602600 -1 chr15 8 NM_001001409 38023452 38029815 1 chr20 9 NM_001001501 3187183 3217911 -1 chr6 [[alternative HTML version deleted]]