I am using simpleaffy using R studio in windows. I've set my working directory and my covdesc.txt file is in the directory:

> dir()
[1] "covdesc.txt"   "GSM413159.CEL" "GSM413160.CEL" "GSM413161.CEL" "GSM413165.CEL"
[6] "GSM413166.CEL" "GSM413167.CEL"

However when I try to read the file, it doesn't find it:

> raw.data <-read.affy()
Error in file(file, "rt") : cannot open the connection
In addition: Warning message:
In file(file, "rt") :
  cannot open file './covdesc': No such file or directory

My file is properly formatted. What could be going wrong? 

Thanks

Please have a close look at the error that is returned: cannot open file './covdesc': No such file or directory.

Combine this with the info on the help page (?read.affy):

Usage: read.affy(covdesc = "covdesc",path=".", ...)

In your case you are using a covariate description file that has the extension .txt. By default read.affy expects such file indeed to have the name covdesc, but without any extension. So you will need to remove that (.txt) from your file.

Alternatively, my preferred way; explicitly specify this covdesc file when calling the function, thus read.affy(covdesc = "covdesc.txt")