[BioC] error while using genefilter's nsFilter: could not find function "hgug4112a.db_dbconn"

[James F. Reid]

Hi,

I think Massimo is using a custom chip and has prepared it using 
SQLForge: hgug4112a.db_2.3.5 is present in the sessionInfo().
The solution is to remove the '.db' from the annotation of your 
ExpressionSet, here is an example with sample data:

Best,
J.

library("Biobase")
data(sample.ExpressionSet)
print(annotation(sample.ExpressionSet))
##[1] "hgu95av2"
library("hgu95av2.db")
library('genefilter')

esetPROC <- sample.ExpressionSet
esetGSEA <- nsFilter(esetPROC,
                      require.entrez=TRUE,
                      require.GOBP=TRUE,
                      remove.dupEntrez=TRUE,
                      var.func=IQR, var.cutoff=0.5)
## ok
print(esetGSEA$filter.log)
##$numLowVar
##[1] 119
##
##$numDupsRemoved
##[1] 24
##
##$feature.exclude
##[1] 19
##
##$numNoGO.BP
##[1] 53
##$numRemoved.ENTREZID
##[1] 166

annotation(esetPROC) <- "hgu95av2.db"
esetGSEA <- nsFilter(esetPROC,
                      require.entrez=TRUE,
                      require.GOBP=TRUE,
                      remove.dupEntrez=TRUE,
                      var.func=IQR, var.cutoff=0.5)

##not ok
##Error in do.call(paste(chip, "_dbconn", sep = ""), list()) :
##  could not find function "hgu95av2.db_dbconn"

sessionInfo()
R version 2.10.0 (2009-10-26)
i486-pc-linux-gnu

locale:
  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
  [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] genefilter_1.28.0   hgu95av2.db_2.3.5   org.Hs.eg.db_2.3.6
[4] RSQLite_0.7-3       DBI_0.2-4           AnnotationDbi_1.8.0
[7] Biobase_2.6.0

loaded via a namespace (and not attached):
[1] annotate_1.24.0 splines_2.10.0  survival_2.35-7 tools_2.10.0
[5] xtable_1.5-5


James W. MacDonald wrote:
> Hi Massimo,
> 
> Massimo Pinto wrote:
>> Greetings all,
>>
>> I have finally come across to genefilter's nsFIlter(); it looks like
>> it's going to do quite a lot for me in just one call.  I called it as
>> follows:
>>
>>> esetGSEA <- nsFilter(esetPROC, require.entrez=TRUE, 
>>> require.GOBP=TRUE, remove.dupEntrez=TRUE, var.func=IQR, var.cutoff=0.5)
>> Error in do.call(paste(chip, "_dbconn", sep = ""), list()) :
>>   could not find function "hgug4112a.db_dbconn"
> 
> This could probably use a better error message. The problem is that you 
> don't have the annotation package for this chip available, so you cannot 
>  filter based on things like Entrez Gene, GO BP, etc.
> 
> I assume this is a custom chip, so you will need to get the annotation 
> file from Affy and build an annotation package yourself using SQLForge. 
> See the SQLForge vignette for more information:
> 
> http://www.bioconductor.org/packages/release/bioc/vignettes/AnnotationDbi/inst/doc/SQLForge.pdf 
> 
> 
> Best,
> 
> Jim
> 
> 
>>
>>> annotation(esetPROC)
>> [1] "hgug4112a.db"
>>
>> here's some info on my session:
>>
>>> sessionInfo()
>> R version 2.10.0 (2009-10-26)
>> x86_64-apple-darwin9.8.0
>>
>> locale:
>> [1] C
>>
>> attached base packages:
>> [1] grid      tcltk     stats     graphics  grDevices utils
>> datasets  methods   base
>>
>> other attached packages:
>>  [1] affy_1.24.0             gplots_2.7.3            caTools_1.10
>>       bitops_1.0-4.1          gdata_2.6.1             gtools_2.6.1
>>  [7] hgug4112a.db_2.3.5      org.Hs.eg.db_2.3.6      RSQLite_0.7-3
>>       DBI_0.2-4               Agi4x44PreProcess_1.5.1
>> genefilter_1.28.0
>> [13] annotate_1.24.0         AnnotationDbi_1.7.20    limma_3.2.1
>>       Biobase_2.6.0
>>
>> loaded via a namespace (and not attached):
>> [1] affyio_1.13.5        preprocessCore_1.7.9 splines_2.10.0
>> survival_2.35-7      tools_2.10.0         xtable_1.5-5
>>
>> Thanks a lot,
>> Yours
>> Massimo
>>
>> Massimo Pinto
>> Post Doctoral Research Fellow
>> Enrico Fermi Centre and Italian Public Health Research Institute 
>> (ISS), Rome
>> http://claimid.com/massimopinto
>>
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>