[BioC] Error loading, on Bioconductor 1.8, exprSet generated with bioconductor 1.7

James W. MacDonald jmacdon at med.umich.edu
Thu Jun 8 14:56:14 CEST 2006

Hi Raffaele,

rcaloger wrote:
> However, this problem rise the question: is ti reasonable to use exprSet 
> objects as backup?

There are (at least) two ways to save the results of an analysis. The 
first is to save your workspace as a binary .RData object, and load it 
later if you want to do more work, etc. I have no idea if this is a 
common thing to do, but you can run into the problems you have 
experienced if you do so. Personally, I have never used this approach, 
and I would bet that is true of most experienced R users.

The second is to save the code you used to do the analysis. If you want 
to re-run the analysis or do more work, all you have to do is source() 
the code and then continue on. The obvious downside of this approach is 
the time required to re-run the code. However, I find that the vast 
majority of the analyses I do can be re-run in a matter of minutes. If I 
have something that took a long time to run, I will usually write the 
results to disk (using write.table()), and then I can use read.table() 
to read it back in.

Using some sort of R-aware editor such as (X)emacs/ESS makes saving your 
code much more straightforward, not to mention all the niceties such as 
parentheses matching, highlighting, etc.



> Thanks for your help
> Raffaele

James W. MacDonald, M.S.
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

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