Dear all, I am using the Arabidopsis affymetrix microarray and I would like to collect the probeset positions on the genome. I used ath1121501.db and strangely, I got negative positions.... Is this normal?? >library(ath1121501.db) >kchrl=mappedkeys(ath1121501CHRLOC) > get(kchrl[2],ath1121501CHRLOC) 1 -11649 > sessionInfo() R version 2.8.0 (2008-10-20) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=en_US;LC_COLLATE=en_US;LC_MONETARY =C;LC_MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHON E=C;LC_MEASUREMENT=en_US;LC_IDENTIFICATION=C attached base packages: [1] tools stats graphics grDevices utils datasets methods [8] base other attached packages: [1] ath1121501.db_2.2.7 RSQLite_0.5-6 DBI_0.2-3 [4] AnnotationDbi_1.4.3 Biobase_2.2.2 -- ================================================================== Na?ra Naouar Tel:+32 (0)9 331 38 63 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM nanao at psb.vib-ugent.be http://www.psb.vib- ugent.be

Sorry, I haven't read the manual :( It's simply to to the fact that the gene is in the other strand!!! Good luck to all with your work!!! Naira Naira Naouar wrote: > Dear all, > > I am using the Arabidopsis affymetrix microarray and I would like to > collect the probeset positions on the genome. > I used ath1121501.db and strangely, I got negative positions.... > Is this normal?? > > >library(ath1121501.db) > >kchrl=mappedkeys(ath1121501CHRLOC) > > get(kchrl[2],ath1121501CHRLOC) > 1 > -11649 > > sessionInfo() > R version 2.8.0 (2008-10-20) > x86_64-unknown-linux-gnu > > locale: > LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=en_US;LC_COLLATE=en_US;LC_MONETA RY=C;LC_MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELEPH ONE=C;LC_MEASUREMENT=en_US;LC_IDENTIFICATION=C > > > attached base packages: > [1] tools stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] ath1121501.db_2.2.7 RSQLite_0.5-6 DBI_0.2-3 > [4] AnnotationDbi_1.4.3 Biobase_2.2.2 > > > > > -- ================================================================== Na?ra Naouar Tel:+32 (0)9 331 38 63 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM nanao at psb.vib-ugent.be http://www.psb.vib- ugent.be