Error in file(file, "rt") : cannot open the connection
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8.3 years ago

Hey, I am new in this R world. I am doing work on MicroRNA dataset with ExiMir package. My dataset is in the form of ImaGene TXT format. As described in the package, I make a folder named Exiqon and paste all relevant data there, set working directory on R and start working. But when I want to read all my files it shows error - Error in file (file, "rt") : cannot open the connection. I check my current working directory, set all files clearly there still facing the same issue.

I use this code

make.gal.env(galname = 'galenv')

ebatch <- ReadExi(txtfile.path = "D:/R/Exiqon", galname = "galenv")

and get the error

Read header information
Read D:/R/Exiqon/GSM1302311_0_Exiqon_14173049_S01.txt 
Error in file(file, "rt") : cannot open the connection
In addition: Warning message:
In file(file, "rt") :
cannot open file 'D:/R/Exiqon/NA': No such file or directory

What should I do now?

Thank you in advance.

R MicroRNA TXT FORMAT • 21k views
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This is really an R question. The error is also very informative. It tries to open a file that does not exist.

cannot open file 'D:/R/Exiqon/NA': No such file or directory
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I am working in D:/R/Exiqon, the working directory in R also D:/R/Exiqon, then why it is giving the error D:/R/Exiqon/NA

Even, in my code also, I specify my path of work. there is no NA folder within Exiqon

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NA is typically generated when data is missing, NA = not a number. I think whatever you pass to the function (in this case galname) is not set up correctly. You should ask this question on the Bioconductor support forum:

https://support.bioconductor.org/

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Okay, I also think that the issue may be in gal file or in samplesinfo.txt file. But I cross-checked both the files and they look fine. Otherwise Thank you for replying. I will post my question on Bioconductor support forum.

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