[BioC] XPS with Arabidopsis Gene 1.1 ST Array Strip

[cstrato]

Dear Benedikt,

I am glad that you have found a way to solve the problem, i.e. using 
PowerTools apt-cel-convert.

If you look at the site for the Affymetrix Calvin Generic Data File 
Format, see:
http://www.jotternotes.com/R/affxparser/Affymetrix_200811-FileFormats/generic.html
you will see that for strip arrays more than one Data Group is allowed. 
For normal arrays and plate arrays there is always only one Data Group, 
and thus I did implement the C++ code only for one Data Group. For this 
reason you did get the error: Number of data groups is not 1!

Best regards,
Christian

P.S.: I am cc to BioC as information for other users of xps.


On 7/10/14 2:47 PM, Benedikt Athmer wrote:
> Dear Christian,
>
> I circumvent this problem by converting the cel-files (using Affymetrix
> PowerTools apt-cel-convert -f text -o text_outdir *.cel) to text-cel
> files. XPS does now import the text-cel files. I downloaded some
> examples files from the affymetrix
> (http://www.affymetrix.com/catalog/prod530004/AFFY/Model-and-applied-research-organisms-Gene-1.1-ST-Array-Strips#1_3)
> where you can also find the library and annotation files. I'm still
> explore the xps-package, I will get in touch with you, if there is
> another problem,
>
> Benedikt
>