>Hello Group, > How can I get RefSeq accession IDs instead of LocusLink IDs. If you have the devel version of data package installed, you can do: >get("1000_at", env=hgu95av2REFSEQ) [1] "NM_002746" "NP_002737" "NM_002746" "NP_002737" Otherwise, you have to do >library(reposTools) >install.packages2("hgu95av2", develOK = TRUE) first. > >>get("1000_at", env=hguav2LOCUSID) >[1] 5595 > >Instead of one single probe, how can I get all 12,625 in RefSeq accession ID for hguav952. > >env=hguav2REFSEQ isnt working. > >Please help. > >Thank you. > > >Robert Baertsch <baertsch@soe.ucsc.edu> wrote: >While you are at it, can you please allow people to install R without >being root? Our sysadmin will install only RPMs and since bioconductor >has no RPMS, all of the R users need to compile the source for R. > >It is a real pain and many long time R users are frustrated by it. What >do you guys have to do something special? Every other unix app in the >world has an RPM. > >RPM good. >installation scripts bad. > >Get the picture. > >Jeff Gentry wrote: > >>>I've gotten this error a few times. Each time I rerun getBioC("exprs") , >>>it get past it and then it happens again. >>> >>> >> >>Yes ... I've gotten a rash of these reports, have not been able to >>personally reproduce it. Originally the first couple of people were using >>Mac OS X, so thought it was a problem specific to that OS, but now have a >>few people using Win32 and Unix machines. I'm a bit baffled as everyone >>is using release side stuff, and nothing should have changed there, but >>clearly something is not right. Will let folks know ASAP when I figure >>something out. >> >>Thanks >>-J >> >> > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor > > >--------------------------------- > > > [[alternative HTML version deleted]] > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor Jianhua Zhang Department of Biostatistics Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084

Dear Dr. Zhang, thank you for your suggestion. It is quite a problem for LocuLink IDs that have many splice forms (with different NM_ entries for one single LocusLink ID). In this case is there a method to ask only the longest form of the transcript should be written to the row linked to specific affy probe, intead of all splice forms writing to that row. thank you. Kind regards Ranga > x2.x3.refseq.data.frame <-data.frame(refseqID,x2.x3.exp.fc,pvals.x2.x3) Error in data.frame("1114_at" = c("NM_001202", "NP_001193", "NM_130850", : arguments imply differing number of rows: 12, 1, 4, 18, 8, 6, 2, 20, 7, 10, 16, 32, 24, 28, 5, 22, 9, 3, 40, 36, 17, 14, 42, 84, 30, 44, 34, 19, 45, 52, 13, 56, 76, 72, 11, 48, 60, 26, 21 John Zhang <jzhang@jimmy.harvard.edu> wrote: >Hello Group, > How can I get RefSeq accession IDs instead of LocusLink IDs. If you have the devel version of data package installed, you can do: >get("1000_at", env=hgu95av2REFSEQ) [1] "NM_002746" "NP_002737" "NM_002746" "NP_002737" Otherwise, you have to do >library(reposTools) >install.packages2("hgu95av2", develOK = TRUE) first. > >>get("1000_at", env=hguav2LOCUSID) >[1] 5595 > >Instead of one single probe, how can I get all 12,625 in RefSeq accession ID for hguav952. > >env=hguav2REFSEQ isnt working. > >Please help. > >Thank you. > --------------------------------- [[alternative HTML version deleted]]

>It is quite a problem for LocuLink IDs that have many splice forms (with different NM_ entries for one single LocusLink ID). In this case is there a method to ask only the longest form of the transcript should be written to the row linked to specific affy probe, intead of all splice forms writing to that row. No, we annotate probes based on what LocusLink gives. I am afraid that you will have to figure out which of the RefSeq is the longest. > >thank you. > >Kind regards >Ranga > > >> x2.x3.refseq.data.frame <-data.frame(refseqID,x2.x3.exp.fc,pvals.x2.x3) >Error in data.frame("1114_at" = c("NM_001202", "NP_001193", "NM_130850", : > arguments imply differing number of rows: 12, 1, 4, 18, 8, 6, 2, 20, 7, 10, 16, 32, 24, 28, 5, 22, 9, 3, 40, 36, 17, 14, 42, 84, 30, 44, 34, 19, 45, 52, 13, 56, 76, 72, 11, 48, 60, 26, 21 > > > > > > > > > > > > > > > > > > > >John Zhang <jzhang@jimmy.harvard.edu> wrote: > >>Hello Group, >> How can I get RefSeq accession IDs instead of LocusLink IDs. > >If you have the devel version of data package installed, you can do: > >>get("1000_at", env=hgu95av2REFSEQ) >[1] "NM_002746" "NP_002737" "NM_002746" "NP_002737" > >Otherwise, you have to do >>library(reposTools) >>install.packages2("hgu95av2", develOK = TRUE) > >first. > >> >>>get("1000_at", env=hguav2LOCUSID) >>[1] 5595 >> >>Instead of one single probe, how can I get all 12,625 in RefSeq accession ID >for hguav952. >> >>env=hguav2REFSEQ isnt working. >> >>Please help. >> >>Thank you. >> > > >--------------------------------- > > > [[alternative HTML version deleted]] > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor Jianhua Zhang Department of Biostatistics Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084