Error in file(file, "rt") : cannot open the connection - Using ExiMir Package
Entering edit mode
Last seen 6.5 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 = '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? Maybe the issue in gal file or in sampleinfo.txt file, but I fail to understand the problem.

Thank you in advance.

R eximir microrna • 2.5k views
Entering edit mode

My samplesinfo file has Hy3 txt file but I don't have Hy5 file in my dataset. Is this creating error? 


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