Problem in reading the NCBI's GEO microarray SOFT files in R/BioConductor

Question

[aswathym]

I was working in R reading the GEO dataset. I don't know why I can't execute this command. I don't know whether it is any installation problem or any library missing .I am using dataset from GEO database. This is the first time I am trying in R

looking forward for the answers..

geneNames(eset)[1:10]
Error: could not find function "geneNames"

[PoGibas]

Are you following any tutorial? Where did you get those lines?

[aswathym]

Yeah I was following one tutorial. i loaded GEO file and checked the metadata everything was fine.

eset <- GDS2eSet(gds858, do.log2=TRUE)

This is what I did before running geneNames() function

Do you think its bcoz of library intsllation problem in R

When I tried to upgrade. I got this.

Error: Bioconductor version 3.0 cannot be upgraded with R version 3.1.0

[PoGibas]

No, it's not library installation problem. This function was "Biobase Deprecated and Defunct".

[aswathym]

So what do you think - how should I proceed?

Answer 1

[Sean Davis]

The method is featureNames(), not geneNames(). Try that instead.

If you are looking for actual gene symbols, you'll need to use fData(eset)[1:10,] and determine which column you would like to use for "gene name".