[R] R cannot find the path on my mac

Gitte Brinch Andersen GITTEBA at HUM-GEN.AU.DK
Wed Apr 24 17:46:10 CEST 2013


I am really sorry for this probably quite simple question.
I am new to R, and I am running a pipeline that has already been made. All I have to do is give the paths for different folders, where the pipeline can find the files with my data.

But every time I try to run the pipeline it returns with the message, that it cannot find the file. And I really don't know why. I have found the path by going to the folder and finding the info about the folder, where the location of this is stated. I copy-paste this into the source command.

The path for the folder is:

When found with the "info about the folder":
/Users/gban/Desktop/Methylation analysis/MethylationDataAnalysis

But I think it should be:
/Users/gban/Desktop/Methylation analysis/MethylationDataAnalysis/1.Normalization_raw_data/
as it is the folder 1.Normalization_raw_data where my data are in.

I have tried both paths but it returns with this message every time:

> source('/Users/gban/Desktop/Methylation analysis/MethylationDataAnalysis/1.Normalization_raw_data/pipelineIlluminaMethylation.main.R')
Fejl i file(filename, "r", encoding = encoding) : 
  cannot open the connection
In addition: Advarselsbesked:
In file(filename, "r", encoding = encoding) :
  cannot open file '/Users/gban/Desktop/Methylation analysis/MethylationDataAnalysis/1. 450K_pipeline_Nov2012release./SRC/loadMethylumi2.R': No such file or directory

Do you have any idea why? 
I know this is probably more a question of how to type the path on a mac, than it is a question of how R works.

But I am really frustrated about this, and thought it might be possible for you to help?

Thank you in advance, and again sorry for the quite stupid question.


Gitte Brinch Andersen

E-mail: gitteba at hum-gen.au.dk

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