[BioC] hgug4845a.db - error in the lookUp function when running genes.rpt.agi

[James W. MacDonald]

Hi Adriana,

On Wednesday, October 09, 2013 11:17:35 AM, Pitea Adriana wrote:
> Hi all,
>
>
>   When trying to identify different probes that interrogate the same gene for hgug4845a.db instead of hgug4112a.db, as it follows:
>
>
> library(hgug4845a.db) #<== This package contains the annotation information for the used rat arrays http://www.bioconductor.org/packages/release/data/annotation/
> CV.rep.probes(dd,"hgug4845a.db",foreground="MeanSignal", raw.data=TRUE, writeR=T, targets)
>
> genes.rpt.agi(dd,"hgug4845a.db",raw.data=TRUE, WRITE.html=TRUE,REPORT=TRUE)
>
> I get the following error:
>
> Error in lookUp(PROBE_ID, annotation.package, "SYMBOL") :
>    No keys provided

This is caused by this part of the code in genes.rpt.agi():

 GENE_ID = unlist(lookUp(PROBE_ID, annotation.package, "ACCNUM"))

These GENE_IDs are then used to filter the PROBE_IDs down to unique 
genes. Unfortunately, there are no GENE_IDs!

> head(toTable(hgug4845aACCNUM))
[1] probe_id  accession
<0 rows> (or 0-length row.names)

The ACCNUM table is empty, which is probably not correct. You have two 
choices; contact the maintainer of this package (you can get his email 
by using packageDescription("hgug4845a.db")$Maintainer), and see if he 
can help you, or you can get the annotation data for this array from 
Agilent, and use the AnnotationForge package to create your own 
annotation package.

Best,

Jim



>
>
> I say that genes.rpt.ago uses this lookUp function, but what should I give as keys for the SYMOBOL parameter?
>
>
> Thank you.
>
> Best wishes,
> Adriana
> 	[[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