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)

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'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Warning: namespace ‘ggplot2’ is not available and has been replaced
by .GlobalEnv when processing object ‘p’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
> 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@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(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
>> â€˜dbGetPreparedQueryâ€™ for
>> signature â€˜"SQLiteConnection", "character", "integer"â€™
>>
>> *
>>
>> 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
>

	[[alternative HTML version deleted]]

