Error in limma: maimages (cannot open the connection)
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7.4 years ago
naving2uk ▴ 10

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

R • 2.5k views
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I used this code

filesAd <- list.files(".", all.files = TRUE, full.names = TRUE)


and the error is:

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

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

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7.4 years ago

Most likely, you are specifying the path to the file incorrectly or there is a permission problem. Print the value of targets$FileName and look on your hard drive to see whether the file exists, and whether you have read permissions for that file. ADD COMMENT 0 Entering edit mode I used targets$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"


:(

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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

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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.