[BioC] CORNA and biomaRt packages. miRNA and mRNA expression comparation

[James MacDonald]

You can install a source package on any platform; for windows it just
happens to take a bit of work, although these days it is only a trivial
amount of work. See here

http://cran.r-project.org/bin/windows/base/rw-FAQ.html#Can-I-install-packages-into-libraries-in-this-version_003f

Best,

Jim



James W. MacDonald, M.S.
Biostatistician
Douglas Lab
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
>>> Jordi Altirriba 11/25/10 4:18 AM >>> 

Dear Bioconductor users, 
I am trying to work with CORNA.1.2. package to observe how miRNA
regulates mRNA expression levels, as described in Wu X, Watson M, CORNA:
testing gene lists for regulation by microRNAs, Bioinformatics. 2009 Mar
15;25(6):832-3. 
I have downloaded this package from the authors’ webpage:
http://corna.sourceforge.net/ 
Nevertheless, this package was compiled with a version previous than
R.2.10.0, so I am not able to run it in R.2.12.0 version (current
version). 
I have downloaded R.2.9.0 version and I am able to load CORNA package
but biomaRt is not running (BioMart web service failed) [sessionInfo
below]. 
It’s not a problem of BioMart web service, as in R.2.12.0 BioMart is
running correctly. 
My questions: 
1.- Is there any way to run BioMart in previous versions of R? (R.2.9.0
or previous) 
2.- If it’s not possible, could I recompile CORNA package to run in
R.2.12.0? How? 
3.- Is there any other package to associate miRNA expression levels from
microarrays with mRNA expression levels from other microarrays? (I am
working with rats and mice and MMIA is not working with these species) 
Many thanks for your time and suggestions. 
Yours faithfully, 

Jordi Altirriba 
Laboratoire du Métabolisme 
Centre Médical Universitaire 
Geneve 

> sessionInfo() 
R version 2.9.0 (2009-04-17) 
i386-pc-mingw32 
locale: 
LC_COLLATE=French_Switzerland.1252;LC_CTYPE=French_Switzerland.1252;LC_MONETARY=French_Switzerland.1252;LC_NUMERIC=C;LC_TIME=French_Switzerland.1252

attached base packages: 
[1] tools stats graphics grDevices utils datasets methods base 
other attached packages: 
[1] CORNA_1.2 XML_2.5-1 GEOquery_2.8.0 RCurl_0.98-1 bitops_1.0-4.1
biomaRt_2.0.0 Biobase_2.4.1 


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