Entering edit mode
7.0 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.
This is really an R question. The error is also very informative. It tries to open a file that does not exist.
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
NAis 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:
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.