Ringo File Opening Error
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@gauravgunjal-8870
Last seen 7.0 years ago
India

I am trying to analyze Nimbelgen chip-chip data with "Ringo". I am getting error in the following command. Can anyone please help me.

>exRG <- readNimblegen("example_targets.txt","spottypes.txt",path=exDir)

Reading targets file...
Reading raw intensities...
Error in file(file, "r") : cannot open the connection
In addition: Warning message:
In file(file, "r") :
  cannot open file '/home/linux-gnu-library/3.1/Ringo/exData/Cy3_pair.txt ': No such file or directory.

How to eliminate such error and proceed. Also if anyone have detailed thread/protocol of "Ringo" please share.

Thank you,

Gaurav

India.

 

Ringo • 867 views
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Entering edit mode
Dan Tenenbaum ★ 8.2k
@dan-tenenbaum-4256
Last seen 19 months ago
United States

I recommend you upgrade to the current release of Bioconductor (3.1) which requires R-3.2 ( R version 3.2.2 is recommended).

I was able to get the line in question to work with that version. Of course you need to specify exDir as follows:

 exDir <- system.file("exData",package="Ringo")

 

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