[R] Obtaining Midas and splice index values in onechannelGUI

From: Schraga Schwartz <Schragas_at_post.tau.ac.il>
Date: Mon, 21 Jan 2008 15:27:44 +0200


Hello,  

I've meanwhile got onechannelGUI running (my OS is windows). I'm trying to use it for the analysis of human exon arrays. I was able to load cel files and run them through affymetrix power tools, to obtain normalized affy data. My next step was trying to find differentially spliced exons. The menu offers to calculate either Midas or splice index scores. However, when I try to use Midas, I get the following error message:  

Midas alternative splice analysis started........  

FATAL ERROR: .\TsvFile\TsvFile.cpp:1923: open: Could not open file:
'C:/PROGRA~1/R/R-26~1.1/library/oneChannelGUI/affylibs/' to read.

....saving MiDAS p-values

Error in assign("midas.p", midas.p, affylmGUIenvironment) :

  object "midas.p" not found

In addition: Warning messages:

  1. In file(con, "r") :

  file("") only supports open = "w+" and open = "w+b": using the former

2: In file(con, "w") :

  file("") only supports open = "w+" and open = "w+b": using the former

3: In dir(libDir) :

  list.files: 'C:/PROGRA~1/R/R-26~1.1/library/oneChannelGUI/affylibs/' is not a readable directory

4: In file(file, "r") :

  cannot open file
'D:/LabStuff/Slu7/OneChannelGUI/outMidas66c4366b/midas.pvalues.txt', reason
'No such file or directory'
 

Please note that it is unclear to me why the program is searching the "program files" directory; since R is installed in the C:\R-2.6.  

In addition, when I try to run the splice index menu, the program just gets stuck; and I eventually use ctrl+alt+del to stop R.  

Again, I'd be grateful for any help.  

Thanks,

Schraga Schwartz

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