Dear all, I'm very new to R and BioConductor, but I somehow managed to deal with my ChIP-chip data (normalization and quality controls). The platform is Nimblegen ChIP for E. coli K12. My current problem is that I don't find a way to map my putative peaks to the genome. I tried using biomaRt but its Mart ensembl only allows to access the eukaryotic genomes. Given that there is an entry for E. coli in Ensembl, but it is not taken into account by biomaRt, I don't know how to do this mapping. Do you have any ideas? Thanks a lot in advance! Best, Rayna -- "Change l'ordre du monde plutôt que tes désirs." Membre du CA de l'April - Promouvoir et défendre les logiciels libres ( www.april.org) PhD Student "Molecular Evolution and Bioinformatics" Ludwig-Maximilians University (LMU) of Munich What happens when you've worked too long in the lab : *You wonder what absolute alcohol tastes like with orange juice. *Warning labels invoke curiosity rather than caution. *The Christmas nightout reveals scientists can't dance, although a formula for the movement of hands and feet combined with beats per min is found scrawled on a napkin by a waiter the next day. *When you have twins, you call one of them John and the other - Control. [[alternative HTML version deleted]]

Hi Rayna, Did you check the bacteria ensembl BioMart? If you do: > library(biomaRt) > listMarts() biomart 1 ensembl 2 snp 3 functional_genomics 4 vega 5 bacterial_mart_5 The 5th biomart is the bacteria BioMart of Ensembl. When you select that one and check which datasets it contains I get: > mart=useMart("bacterial_mart_5") > listDatasets(mart) dataset description version 1 str_57_gene Streptococcus pneumoniae TIGR4 genes (EB 1) EB 1 2 esc_20_gene Escherichia coli Sakai genes (EB 1) EB 1 3 myc_25994_gene Mycobacterium bovis Pasteur 1173P2 genes (EB 1) EB 1 4 sta_29522_gene Staphylococcus aureus JH1 genes (EB 1) EB 1 ...... You'll notice there are a few E. Coli strains in there, you can select one as follows: > mart=useMart("bacterial_mart_5",dataset="esc_30585_gene") Checking attributes ... ok Checking filters ... ok To see what kind of data is available do: > listAttributes(mart) > listFilters(mart) And then do your query with getBM Hope this helps, Steffen On Fri, Aug 27, 2010 at 11:05 AM, Rayna <rayna.st@gmail.com> wrote: > Dear all, > > I'm very new to R and BioConductor, but I somehow managed to deal with my > ChIP-chip data (normalization and quality controls). The platform is > Nimblegen ChIP for E. coli K12. > My current problem is that I don't find a way to map my putative peaks to > the genome. I tried using biomaRt but its Mart ensembl only allows to > access > the eukaryotic genomes. Given that there is an entry for E. coli in > Ensembl, > but it is not taken into account by biomaRt, I don't know how to do this > mapping. > > Do you have any ideas? > > Thanks a lot in advance! > > Best, > Rayna > > -- > "Change l'ordre du monde plutôt que tes désirs." > > Membre du CA de l'April - Promouvoir et défendre les logiciels libres ( > www.april.org) > > PhD Student > "Molecular Evolution and Bioinformatics" > Ludwig-Maximilians University (LMU) of Munich > > > > What happens when you've worked too long in the lab : > *You wonder what absolute alcohol tastes like with orange juice. > *Warning labels invoke curiosity rather than caution. > *The Christmas nightout reveals scientists can't dance, although a formula > for the movement of hands and feet combined with beats per min is found > scrawled on a napkin by a waiter the next day. > *When you have twins, you call one of them John and the other - Control. > > [[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]