Question: chippeakanno related
0
8.3 years ago by
Julie Zhu4.1k
United States
Julie Zhu4.1k wrote:
Deepak, 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 Here is an related post http://comments.gmane.org/gmane.science.biology.informatics.conductor/ 28493 I will keep you posted on the new function. Thanks! Best regards, Julie On 8/2/11 12:47 PM, "Deepak Grover.CTR" <deepak.grover.ctr at="" usuhs.mil=""> wrote: > Dear Dr. Zhu, > > Thank you, the conversion will be incredible to have and I will await your > response. > > Meanwhile, I am finding an error while doing the following. Can you suggest a > fix for this. > I really appreciate your response as it will help me to annotate my chip-seq > data. > > x <- > read.table(file="~/projects/chip-seq/H3K4/C2C12-Control- H3K4-W200-G2000-FDR0.0 > 1-island.bed") > > x <- BED2RangedData(x) > Error in rownames<-(*tmp*, value = c("155", "113", "240", "486", "128", : > duplicate rownames not allowed > > attached is the file, if needed. > > > Thanks, > Deepak > > >>>> "Zhu, Lihua (Julie)" 8/1/2011 10:22 AM >>> > Deepak, > > Sorry for the late response! I just got back from the Bioc2011 conference. > > We hope to add the conversion function this week. So I think it is the best > to wait and I will keep you updated! > > Best regards, > > Julie > > > On 7/29/11 10:36 AM, "Deepak Grover.CTR" > wrote: > >> Thank you for the response, Dr. Zhu. >> I will look forward to those updates which bring HUGO sumbols to the table. >> >> I haven't been able to use the getBM command successfully for mouse gene >> symbols. >> Can you suggest me what should the syntax be, if you people have already done >> it. >> >> Thanks again, >> Deepak >> >> >> >> >> >> Classification: UNCLASSIFIED >> Caveats: None >>>>> "Zhu, Lihua (Julie)" 7/28/2011 4:46 PM >>> >> Deepak, >> >> Jianhong is working on adding gene symbol and other IDs to the annotated >> peaks. We will keep you updated. >> >> Meanwhile, you could use getBM function in biomaRt to get gene symbols. >> Thanks! >> >> Best regards, >> >> Julie >> >> >> On 7/28/11 9:50 AM, "Deepak Grover.CTR" wrote: >> >>> Dear Ms. Zhu, >>> >>> I am a researcher working on mouse chip-seq at USUHS, bethesda. I am trying >>> to >>> employ your bioconductor package for the annotation. I am getting gene IDs >>> in >>> ensembl format using TSS.mouse.NCBIM37, however I am looking to do the same >>> to >>> get back gene symbols(HUGP/hgnc). Can you suggest if there is a quickfix for >>> this. >>> I was trying convert bed format data for mouse gene annotation using >>> "BED2RangedData" but so far did not succeed as that is giving me duplicate >>> row >>> name error. >>> >>> I will really appreciate if you can suggest an easy fix to my problem. >>> >>> Best, >>> >>> >>> >>> Deepak Grover, Ph.D. >>> Scientist >>> Department of Anatomy, Physiology & Genetics >>> Uniformed Services University of the Health Sciences >>> Room C-2070 >>> 4301 Jones Bridge Rd Bethesda, MD 20814 >>> 301-295-3817 >>> Deepak.Grover.CTR at usuhs.mil >>> http://www.usuhs.mil/ >>> >>> >>> >>> >>> Classification: UNCLASSIFIED >>> Caveats: None >>> >>> >>> >>> Classification: UNCLASSIFIED >>> >>> Caveats: None >>> >>> >>> >> >> >> >> >> Classification: UNCLASSIFIED >> >> Caveats: None >> >> >> > > > > > > > Classification: UNCLASSIFIED Caveats: None ??