Question: Problem in reading the NCBI's GEO microarray SOFT files in R/BioConductor
0
gravatar for aswathym
5.2 years ago by
aswathym0
United States
aswathym0 wrote:

I was working in R reading the GEO dataset .I don't know why I cant execute this command. I dont 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"

R • 2.5k views
ADD COMMENTlink modified 5.1 years ago by Biostar ♦♦ 20 • written 5.2 years ago by aswathym0

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

ADD REPLYlink written 5.2 years ago by PoGibas4.8k

ya 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

 

ADD REPLYlink written 5.2 years ago by aswathym0

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

ADD REPLYlink written 5.2 years ago by PoGibas4.8k

so what you think..

how i should proceed

ADD REPLYlink written 5.2 years ago by aswathym0
2
gravatar for Sean Davis
5.2 years ago by
Sean Davis25k
National Institutes of Health, Bethesda, MD
Sean Davis25k wrote:

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".

ADD COMMENTlink written 5.2 years ago by Sean Davis25k
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