[BioC] RSQLite and DB problems
James W. MacDonald
jmacdon at uw.edu
Mon Sep 30 17:17:07 CEST 2013
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
>
> any(is.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]]
>
>
>
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>
> --
> 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
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