Question: Can't Use "getGEO" Command Function in R Program
0
gravatar for drobinson289
13 months ago by
drobinson2890 wrote:

Good Afternoon Everyone,

I have been using R Program, Bioconductor, and GEO Query to analyze some NCBI GEO Microarray Datasets for a few months now.

The current R Program Versions I have been using have been Version 3.4.1 and Version 3.4.4. The Bioconductor Version that has been available for use for this R Program versions on my personal computer and laboratory computer is Bioconductor 3.6.

I have been experiencing a problem with using the "getGEO" command function in the R Program. Whenever I load all of the required packages needed, update all of the sources according to the request of the R program,   and then try to use getGEO to upload the microarray expression set (both GDS and GSE Series Matrix/SOFT Family Files), the R Program responds back saying that the "getGEO function" cannot be found.

This problem started yesterday evening and has never happened to me while using GEOQuery, Bioconductor, or R Program.

I have typed out my coding below:

> source("http://www.bioconductor.org/biocLite.R")

> biocLite()

> biocLite("GEOquery")

> library(GEOQuery)

> getPackageIfNeeded <- function(pkg){if(!require(pkg,character.only = TRUE))biocLite(pkgs=pkg)}

> sapply(pkgs,getPackageIfNeeded)

>library(Biobase)

> library(limma)

> library(affy)

> gset <- getGEO("GSE69033", GSEMatrix =TRUE)

> gse <- getGEO("GSE69033", GSEMatrix =TRUE)

Questions: 

1. Was there some kind of program update with R Program to where the getGEO function does not work anymore with Bioconductor or GEOQuery?

2. Is there something wrong with my scripting or coding? Is there something missing or is there something that is not supposed to be there?

3. Is there another way to upload NCBI GEO Microarray Datasets into R Program without the getGEO function?

4. Do any of you recommend any Gene Expression Analysis Techniques from MATLAB or Python? If so, could you mention a link to a coding script for either of those software programs?

Any help or direction in regards to my questions would be greatly appreciated. Thank you so much and I am very glad to be a part of this forum. 

 

ADD COMMENTlink modified 13 months ago by James W. MacDonald50k • written 13 months ago by drobinson2890
Answer: Can't Use "getGEO" Command Function in R Program
0
gravatar for James W. MacDonald
13 months ago by
United States
James W. MacDonald50k wrote:

Please remember that R is case sensitive, and GEOquery is not the same as GEOQuery. So

> biocLite("GEOquery")
> library(GEOQuery)

Will download and install the GEOquery package, and the second call will result in an error:

> library(GEOQuery)
Error in library(GEOQuery) : there is no package called 'GEOQuery'

Which you didn't include in your code example, but would have been there. Using 

> library(GEOquery)

Should set things right.

ADD COMMENTlink written 13 months ago by James W. MacDonald50k

Thank you for your comment. MATLAB and Python are really good about pointing those types of bugs out. I will try this and let you all know if it works. Thanks again. 

ADD REPLYlink written 13 months ago by drobinson2890
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