Hi Assa, On 9/30/2013 11:08 AM, Assa Yeroslaviz wrote: > Hi, > > I did it again in a new session. I get the same results again. Here is > the complete output of the new session: > > Last login: Mon Sep 30 14:42:52 on ttys000 > USER-imac:~ USER$ R > > R version 3.0.1 (2013-05-16) -- "Good Sport" > Copyright (C) 2013 The R Foundation for Statistical Computing > Platform: x86_64-apple-darwin10.8.0 (64-bit) > > R is free software and comes with ABSOLUTELY NO WARRANTY. > You are welcome to redistribute it under certain conditions. > Type 'license()' or 'licence()' for distribution details. > > Natural language support but running in an English locale > > R is a collaborative project with many contributors. > Type 'contributors()' for more information and > 'citation()' on how to cite R or R packages in publications. > > Type 'demo()' for some demos, 'help()' for on-line help, or > 'help.start()' for an HTML browser interface to help. > Type 'q()' to quit R. > > Warning: namespace ?ggplot2? is not available and has been replaced > by .GlobalEnv when processing object ?p? > [Previously saved workspace restored] > > > > > > > library(biomaRt) > > ensembl <- useMart("ensembl", dataset="hsapiens_gene_ensembl") > > theIDs <- getBM(attributes="affy_huex_1_0_st_v2", > + filters="entrezgene",values=10948, mart=ensembl) > > names(theIDs) <- 'psets' > > theIDs > psets <na> <na> <na> <na> <na> <na> <na> <na> <na> > 3720380 3720356 3720363 3720372 3720377 3720358 3720375 3720344 > 3720365 3720353 > <na> <na> <na> <na> <na> <na> <na> <na> <na> <na> > 3720352 3720367 3720373 3720368 3720374 3720370 3720351 3720378 > 3720355 3720371 > <na> <na> <na> <na> <na> <na> <na> <na> <na> <na> > 3720369 3720360 3720357 3720362 3720364 3720359 3720361 3720354 > 3720349 3720366 > <na> <na> > 3720350 3720376 OK. I stand corrected, and I didn't closely look at your output last time. On linux you get a data.frame, but on lesser operating systems it appears you get a vector (I tried on Windows as well) ;-D So you need a data.frame theIDs <- data.frame(psets = theIDs) Best, Jim > > sessionInfo() > R version 3.0.1 (2013-05-16) > Platform: x86_64-apple-darwin10.8.0 (64-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] biomaRt_2.16.0 > > loaded via a namespace (and not attached): > [1] RCurl_1.95-4.1 XML_3.95-0.2 > > > > str(theIDs) > Named int [1:32] 3720380 3720356 3720363 3720372 3720377 3720358 > 3720375 3720344 3720365 3720353 ... > - attr(*, "names")= chr [1:32] "psets" NA NA NA ... > > > > I do it the same in another terminal and got the same results. > I don't get a data.frame as a result. > > Can someone explain it to me? > Please, > > > thanks for the help, > Assa > > > On Mon, Sep 30, 2013 at 5:00 PM, James W. MacDonald <jmacdon at="" uw.edu=""> <mailto:jmacdon at="" uw.edu="">> wrote: > > Hi Assa, > > > On Monday, September 30, 2013 9:23:17 AM, Assa Yeroslaviz wrote: > > Hi, > > I'm trying to work with the oligo package and the example > provided in the > pdf file to pre-processing exon arrays. > > I'm following the commands given in the pdf but I get an error > massage when > trying to query my sqllite DB. > > This is what I do: > > library(biomaRt) > ensembl <- useMart("ensembl", dataset="hsapiens_gene_ensembl") > theIDs <- getBM(attributes="affy_huex_1_0_st_v2", > filters="entrezgene",values=10948, mart=ensembl) > names(theIDs) <- 'psets' > > > Well, I don't think that is actually what you have done, for two > reasons. Number 1, if you had really done so, you would not have > any NA values in your results (biomaRt won't return any NA values > for a query that has a single attribute - it will only return > values that do have a value). Number 2, getBM() returns a > data.frame, which isn't what you show below. > > If I do what you say you did, I get this: > > head(theIDs) > > psets > 1 3720380 > 2 3720356 > 3 3720363 > 4 3720372 > 5 3720377 > 6 3720358 > > anyis.na <http: is.na="">(theIDs)) > > [1] FALSE > > So try again, and if it still doesn't work let us know. > > Best, > > Jim > > > > theIDs > > psets <na> <na> <na> <na> <na> <na> <na> > <na> > <na> > 3720380 3720356 3720363 3720372 3720377 3720358 3720375 > 3720344 3720365 > 3720353 > <na> <na> <na> <na> <na> <na> <na> <na> > <na> > <na> > 3720352 3720367 3720373 3720368 3720374 3720370 3720351 > 3720378 3720355 > 3720371 > <na> <na> <na> <na> <na> <na> <na> <na> > <na> > <na> > 3720369 3720360 3720357 3720362 3720364 3720359 3720361 > 3720354 3720349 > 3720366 > <na> <na> > 3720350 3720376 > > conn <- db(affyExonFS) > fields <- 'meta_fsetid, pmfeature.fsetid, fid, start, stop' > tables <- 'featureSet, pmfeature, core_mps' > sql <- paste("SELECT", fields, > "FROM", tables, > "WHERE pmfeature.fsetid=featureSet.fsetid", > "AND featureSet.fsetid=core_mps.fsetid", > "AND pmfeature.fsetid=:psets") > probesetInfo <- dbGetPreparedQuery(conn, sql, theIDs) > probesetInfo <- dbGetPreparedQuery(conn, sql, > as.data.frame(theIDs)) > > But when I tried this I get the following error massage: > > *Error in (function (classes, fdef, mtable) : > unable to find an inherited method for function > ???dbGetPreparedQuery??? for > signature ???"SQLiteConnection", "character", "integer"??? > > * > > Can anyone explain to me where this error is coming from? Is > it a problem > with the sqlite connection? > > thanks > Assa > > [[alternative HTML version deleted]] > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > > -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099