[BioC] Question on Affxparser (createCel)

[Henrik Bengtsson]

Hi.

On Tue, Aug 5, 2008 at 6:46 AM, Hooiveld, Guido <Guido.Hooiveld at wur.nl> wrote:
>
> As you may recall, I am trying to create CEL files from an AffyBatch
> object (after having my original CEL files be corrected by Harshlight).
> http://article.gmane.org/gmane.science.biology.informatics.conductor/187
> 57
>
> Since my R-skills are very basic, for this I mainly rely on
> understanding examples available in vignettes or BioC mailing list...
> As suggested, I would like to use the 'createCel' and 'updateCel'
> commands from Affxparser.
>
> However, there is one thing in the 'createCel' help page i don't
> understand, which has to do with the type of the CEL file
> (binary,ASCII):
> why should the version of the original input CEL files (that are used as
> template to create the new, updated files) explicity be of version 3
> (type = ASCII?)?
>
> After reading the help page I understand that the OUTPUT cannot be
> anything else than v4 (type = binary), but what about the input? See
> below.

The template CEL header (argument 'header') can be of any version,
i.e. v3 (ASCII), v4 (binary;XDA), or v1 (binary;Calvin).   I have
clarified this in the help(createCel) in the next release/the
developers version.

The easiest is to "reuse" one you get from readCelHeader() of an
existing CEL file

The stopifnot(hdr$version == 3) expression of example(createCel) is
just to assert that the generic code above found an ASCII file.  It is
just to catch stupid mistakes when R CMD check runs.  In the next
release/the developers version, I have added a comment explaining
this.

Hope this helps

Cheers

Henrik

>
> Thanks,
> Guido
>
> <copy/paste from help page 'createCel'>
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # Read the CEL header
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> hdr <- readCelHeader(file)
> stopifnot(hdr$version == 3)
>
>
> ------------------------------------------------
> Guido Hooiveld, PhD
> Nutrition, Metabolism & Genomics Group
> Division of Human Nutrition
> Wageningen University
> Biotechnion, Bomenweg 2
> NL-6703 HD Wageningen
> the Netherlands
> tel: (+)31 317 485788
> fax: (+)31 317 483342
> internet:   http://nutrigene.4t.com <http://nutrigene.4t.com/>
> email:      guido.hooiveld at wur.nl
>
>
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