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

Kasper Daniel Hansen khansen at stat.berkeley.edu
Fri May 21 16:02:24 CEST 2010

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:
> 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

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.


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