[Bioc-devel] Dimension (rows & columns) in the writeCDF function seems to be swapped

[Ben Bolstad]

I don't have specific objections to capitalization. The current
capitalization (initial letter upper-case) is consistent with the
version 3 CEL file format (text).

I see no reasons why these changes can not be batch ported to the
release branch.

Ben

On Fri, 2010-05-21 at 10:02 -0400, Kasper Daniel Hansen wrote:
> On Fri, May 21, 2010 at 3:56 AM, Henrik Bengtsson
> <henrik.bengtsson at gmail.com> wrote:
> > Thanks for this Kasper.
> >
> > Comments below.
> >
> > On Fri, May 21, 2010 at 2:25 AM, Kasper Daniel Hansen
> > <khansen at stat.berkeley.edu> wrote:
> > UPDATE TO AFFYIO:
> > I see that you picked names c("Cols", "Rows") for
> > affyio::read.celfile.header().  In affxparser::readCelHeader() these
> > are labelled *lower-case* c("cols", "rows").  Unless there is a
> > specific reason, I recommend to use the same names in affyio.
> >
> > Other than this, I agree with your update.  Adding names should be
> > safe, especially since you are not changing the order (being explicit
> > about the latter can be useful to add to the NEWS file).   Then
> > packages/functions relying on affyio::read.celfile.header() can start
> > updating their code (and remember to set the correct package
> > dependency in DESCRIPTION).
> >
> > Although it is not a bug in affyio, I also agree that it is worth
> > updating the release version of affyio, because the change will be
> > backward compatible, hence no API change.  Updating the affyio release
> > will help fixing the bug in affy release.
> 
> I was trying to use the same capitalization as the other output of
> read.celfile.header, but I agree that using the same capitalization as
> readCelHeader in affxparser might be better here.  I will change it in
> svn, after the discussion has ended (we still need to hear from
> Ben/Rafa).
> 
> I will also do a grep on any package that depends/suggests/imports
> affyio in order to identify other packages potentially using this
> piece of code.
> 
> Kasper