Drey Drey - 26 days ago 15
R Question

Golub leukemia dataset: Affy IDs to HUGO Symbols (or other)

I have troubles to convert Affy ids to some other standard symbols for further processing:
The data I'm working with is the leukemia data set (Golub et al., 1999).
I use the golubEsets data set retrieved from Bioconductor project.

I tried this tutorial (http://faculty.washington.edu/kenrice/sisg/sisg-sea09-09.pdf)
with

# library for annotation
library("annotate")
library("hgu95av2.db")
library("GO.db")
#library for golub data set
library(golubEsets)
data(Golub_Merge)
geneids <- featureNames(Golub_Merge)
# retrieve something usefull (e.g. gene name)
mget(geneids, hgu95av2GENENAME)


This would produce many errors, because most of the Affy ids in the Golub data set weren't found in the database. Praticularly for this data set, where can I find some standard symbols (HUGO?) - because I need them to conduct further analysis.

Thank you!

Answer

The Golub dataset isn't produced from a hgu95av2 affymetrix chip. It used the older hu6800.

Just typing Golub_Merge at the R command line will give you the summary information and list the Annotation field as "Annotation: hu6800"

See http://bioconductor.org/packages/2.6/data/annotation/html/hu6800.db.html for the correct annotation library.

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