I am struggling to import .gpr raw microarray files from a designated folder and begin the analysis. I can read files, but how do I make a matrix? I loaded marray library, then load the 4 GenePix files, and I need to extract the foreground and background median values from the Cy5 and Cy3 channels.

# accessing     
 dir.path <- ("~/Documents/HW2/")
Reading ...  ~/Documents/HW2//GSM304445.gpr 
Reading ...  ~/Documents/HW2//GSM304446.gpr 
Reading ...  ~/Documents/HW2//GSM304447.gpr 
Reading ...  ~/Documents/HW2//GSM304448.gpr 

# include your problematic code here with any corresponding output

gpr.cdna <- read.HW2(path=dir.path, name.Gf = "F532 Median", name.Gb ="B532 Median", name.Rf = "F635 Median", name.Rb = "B635 Median", name.W ="Flags")

# please also include the results of running the following in an R session 
There were 21 warnings (use warnings() to see them)
> warning(gpr.cdna)
Error in as.character.default(X[[i]], ...) : 
  no method for coercing this S4 class to a vector

sessionInfo( )

The read.maimages() function of the limma package reads gpr files into an appropriate object and performs downstream analysis.

It is not clear what you doing at the moment. As far as I know, there is no function called read.HW2 in any Bioconductor package.