[BioC] problems with Affy vignette and affybatch objects

[Seth Falcon]

Hi Jenny,

Jenny Drnevich <drnevich at uiuc.edu> writes:
> There's some problem with the default value for affybatch objects (if this 
> is the correct description) that's appeared in affy 1.12.0, which also can 
> be seen in the affy vignette. Previously, when I typed in the name of an 
> affybatch object at the command line, I'd get the same output as if I had 
> put 'show(abatch)':

This sounds like a more general issue that is related to changes in R
between 2.3.0 and 2.4.0.  Did you happen to load your "raw" AffyBatch
object from an rda file created with R <= 2.3.x?

What does typeof(raw) report?  When using R 2.4.x, it _should_ report
"S4".  If it does not, it means the object was created using an old
version of R and needs to be updated.

You can try updating it using updateObject (from Biobase):

rare <- updateObject(raw)

> This is also in the vignette (October 3, 2006), on page 11-251 (did 
> no one notice the vignette was 271 pages long?!?). 

Thanks for mentioning this.  We will look into it.  We attempted to
convert all saved objects to the new format, but this suggests that
one or more were missed.

> One last thing - were there no changes to affy for the Bioconductor 1.9 
> release? The beginning of the vignette (Oct 3, 2006) still has listed 
> 'Changes for affy in BioC 1.8 release' in section 2, along with all the 
> same information as in the previous vignette.

Maybe an email to the affy package maintainer is in order ;-)
I happen to know that said maintainer has been busy working on the
oligo package intended to replace the affy package...  But it would be
nice for the documentation to be up-to-date.

Best,

+ seth