Question: Annotation Using GEOquery
gravatar for ekl
4 weeks ago by
ekl0 wrote:

I am trying to finish a microarray analysis. The array I am using does not have an annotation package in Bioconductor. I got the data from GEO NCBI. Now I am trying to annotate the data to be able to find DEGs. How do I go about doing that? Also, when I try to use the read.table function for a txt tile, it says permission denied; see below. Thank you in advance.

Error in file(file, "rt") : cannot open the connection
In addition: Warning message:
In file(file, "rt") :
  cannot open file 'C:\Users\EKL\Downloads\GSE51469_RAW.txt': No such file or directory
annotation txt geo • 62 views
ADD COMMENTlink modified 4 weeks ago by Sean Davis21k • written 4 weeks ago by ekl0

The problems you are having above are not related to Bioconductor. You might want to spend a little time taking a quick intro-to-R course.

ADD REPLYlink written 4 weeks ago by Sean Davis21k
Answer: Annotation Using GEOquery
gravatar for Sean Davis
4 weeks ago by
Sean Davis21k
United States
Sean Davis21k wrote:

As for the annotation from GEOquery, the fData accessor will access the feature data that the submitter supplied to GEO.

g = getGEO("GSE51469")[[1]]

In your case, it appears that the only informative column is the "SEQUENCE" column which you could use to BLAST against genes or genome of interest. Alternatively, write to the submitter of the data to ask for more information about the array platform and features.

ADD COMMENTlink written 4 weeks ago by Sean Davis21k
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