I am trying to process some agilent data by agilp package. I tried the following code to process the raw data

inputdir = file.path("path/to/input/directory")
outputdir = file.path("path/to/output/directory")
AAProcess(input = inputdir, output = outputdir)

And worked fine for me.

But If i try to set the path to one sample  for example

file.path("path/to/input/directory/GSM232970.txt")

I get the error,

Array path/to/input/directory/GSM232970.txt/NAis not present
Error in if (file.exists(inputpath[i])) { : argument is of length zero

Does it mean agilp is not able to read a file from path and must be in the directory?

I also tried to save the output in variable

output <- AAProcess(input = inputdir )

I get NULL as output.

How can I save the output in a variable?

One more thing is, how to generate p-value from raw and processed agilent data.?