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.

corn<-read.table("C:\\Users\\EKL\\Downloads\\GSE51469_RAW.txt",header=TRUE,sep=",")
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

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

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

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.