I'm a new user to MeV. I have four expression microarray experiments that I ran with 3 biological replicates each (Genepix). To analyze these replicates, I was trying to use Rama. I installed the latest MeV (2.5.1) and a slightly older R (2.9.2) and bioconductor (2.4), according to the instructions in the manual. I then in stalled rama, bridge, and Rserve again according to the manual. Starting Rserve from within R worked fine, but starting the daemon from the command prompt using R CMD Rserve didn't work saying it couldn't find the Rserve file. I theb copied Rserve from the R frameworks library to the bin directory, and the daemon started just fine, using port 6311. However, when I loaded my replicated, and started Rama (Adjust Data=>Rama), I got the following error: MeV could not establish a connection with Rserve.
I could not figure out where to look further to trouble shoot this - any ideas?
MacBook Pro, OSX 10.6.2
I apologize for the inconvenience. Unfortunately we do not support RAMA any more as you can find it documented in the Appendix section as:
***Please note that the Rama/Bridge module is no longer supported by MeV***
The RAMA module was written in 2005 with very specific R requirements and no so user friendly set up process.
We left is there as a legacy module and it is upto the user to make it work.
I would suggest you use R directly, also is it possible that you could use another module in MeV in place of RAMA?
Best & Thank you for using MeV.
Hi Raktim -
Bummer. I was not able to find this note in the MeV manual I've been using (for v4.4, 5/28/09). Is there a newer manual?
Also, is there a different MeV module you'd suggest to process biological replicates?
Please refer to the appendix section of the latest MeV (v4.5.1) manual. It should be in the docs directory under MeV folder.
I am not sure if you can do this, but If you can group replicates together then you can look at the some of the algorithms in the "Statistics" category of the drop down menu. Please refer to the manual for detailed description of the methods under the Statistics category.
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