[BioC] error in DEXSeq fitDispersionFunction()

Martin Morgan mtmorgan at fhcrc.org
Mon Aug 13 15:43:15 CEST 2012

On 08/13/2012 05:57 AM, Wolfgang Huber wrote:
> Alejandro Reyes scripsit 08/13/2012 01:12 PM:
>> Dear Georg,
>> Sorry for the delay of my answer.
>> But yes, you have to generate the new ExonCountSet with the new version,
>> or alternatively just do:
> This raises the general question of 'can saved serialised (stored to
> disk) versions of Bioconductor objects be used across different versions
> of the software'?
> The general answer is "no", since anything else would be impractical. In
> particular, package authors may provide facilities for that (e.g. via
> providing a method for the 'updateObject' function in BiocGenerics).
> In general, thus, it is good practice to keep the input data in a
> sufficiently persistent format (e.g. text files) and the code to create
> the objects.
> Others might have further views on this...

Perhaps the best strategy depends on purpose and time scale.

For active research in rapidly changing fields and over 0-2 years it 
seems like portable representation of the original data is best, as 
Wolfgang suggests.

For reproducibility of research in the 1-5 year time span, it seems like 
one would like to archive or retain access to the original software and 
processing scripts, in addition to the data.

Over longer periods it's difficult to find hardware, compilers, etc to 
make use of old software, and perhaps the best bet is archived, updated 
objects like the ALL data set that represent a snapshot of partially 
processed data. This implies that someone with sufficient familiarity 
with the software has been conscientious enough to provide facilities 
for updating objects to work with current implementations, or 
alternatively conservative enough (perhaps because something close 
enough to the 'right' representation has been identified) not to modify 
the underlying data representation.


> Best wishes
>      Wolfgang
> Wolfgang Huber
> http://www.embl.de/research/units/genome_biology/huber
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor

Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793

More information about the Bioconductor mailing list