Assa Yeroslaviz | 30 Sep 15:23 2013
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RSQLite and DB problems

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'

> 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

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