[BioC] Package "xps" problem solved in xps_1.2.1

[cstrato]

For the record:
An updated version xps_1.2.1 is now available from Bioconductor
which can import the new Affymetrix expression annotation files.
Note that only "xxx.na26.annot.csv" expression array files were
affected due to recent changes by Affymetrix, but not the gene
and exon annotation files.

Best regards
Christian


cstrato wrote:
> Dear Caimiao
>
> Although I have tested all annotation files from na21 until na25, I 
> have for some reason never tested the new version na26.
> Sadly, this is the first version where Affymetrix has changed the 
> format of the annotation file.
>
> Luckily, the workaround is simple:
> Please delete the first 12 lines of file 
> "HG-U133_Plus_2.na26.annot.csv" so that the file start with "Probe Set 
> ID".
>
> I have just tested that this solves the problem. In order to see that 
> the annotation file has been imported correctly, you can do:
> export(scheme.hgu133p2.na26, treetype="ann", 
> outfile="HGU133p2_na26_ann.txt")
> This will export the annotation data as text file.
>
> Please let me know if this did solve your problem.
>
> Since you are using xps on Windows here is one suggestion:
> If you run R from Rterm on the Console, you will see all messages when 
> you set "verbose=TRUE", which I would recommend.
>
> Thank you for reporting the problem, I will update my package soon.
>
> Best regards
> Christian
>