Error in limma: maimages (cannot open the connection)

Question

[naving2uk]

I am trying to read and normalize an Agilent dataset but I have this error:

Error in file(file, "r") : cannot open the connection

and also when I tried this code to check the files:

targets$FileName[!file.exists(targets$FileName)]

It works without problems

[naving2uk]

I used this code

filesAd <- list.files(".", all.files = TRUE, full.names = TRUE)
x <- read.maimages(filesAd,source="agilent.median");

and the error is:

Error in file(file, "r") : cannot open the connection
In addition: Warning message:
In file(file, "r") : cannot open file './.': Permission denied

[naving2uk]

I checked the file property for permission, I have normal read \write permission :(

Answer 1

[David Quigley]

Most likely, you are specifying the path to the file incorrectly or there is a permission problem. Print the value of targets$FileName and look on your hard drive to see whether the file exists, and whether you have read permissions for that file.

[naving2uk]

I used targets$FileName the output all the file name with information in targets file?

No problem, and I specify the path:

x <-read.maimages(targets$FileName,path="C:\Users\navin\Desktop\Ad2",source="agilent.median");

but I have this error:

Error: '\U' used without hex digits in character string starting ""C:\U"

:(

[naving2uk]

I am using Rstudio, I put the target file which I create and all the samples file which they are txt file in My Rstudio directory

[David Quigley]

When you write \U you are using the slash as an escape character. I suggest you consult locally with someone who can help you format a path string correctly.