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

James W. MacDonald jmacdon at uw.edu
Wed Oct 9 17:44:31 CEST 2013

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.



> 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]]
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

James W. MacDonald, M.S.
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099

More information about the Bioconductor mailing list