[BioC] problem with xps and annotation file from affymetrix mirna array

[cstrato]

Dear Giacomo,

Steve Shen was so kind to set up centralized scheme file repository at:
http://microarray.bu.edu/~sshen/xps/
so you can download now the scheme "mirna10.root" from this repository.
An official announcement of the availability will follow once the scheme 
list is complete.

Best regards
Christian


On 5/24/10 1:02 PM, giacomo.tuana at unimib.it wrote:
> Dear list,
>
>
>
> I downloaded the three files (cdf, annotation, probes) from Affymetrix
> website; but I got the following error from using xps and mirna
> affymetrix annotation file.
>
> Warning: probeset <mml-miR-1224-star_st> has NumAtoms=4 and NumCells=4
> Warning: probeset <hsa-miR-1226-star_st> has NumAtoms=4 and NumCells=4
> Warning: probeset <hsa-miR-1228-star_st> has NumAtoms=4 and NumCells=4
> Warning: probeset <hsa-miR-664-star_st> has NumAtoms=4 and NumCells=4
> Warning: probeset <mdv1-miR-M9-star_st> has NumAtoms=4 and NumCells=4
> Warning: probeset <cfa-miR-219-star_st> has NumAtoms=4 and NumCells=4
> <52900> records imported...Finished
>     PM/MM statistics:
>        6703 cells with minimum number of PM/MM pairs: 2
>        78 cells with maximum number of PM/MM pairs: 47
> New dataset <miRNA-1_0> is added to Content...
> Importing </home/user/exp/lib/miRNA-1_0.probe.tab> as <miRNA-1_0.prb>...
> Note: The following header columns are missing:
> <Serial Order>
> <46227> records read...Finished
> <52900> records imported...Finished
>     probe info:
>        GC content: minimum GC is <0>  maximum GC is <25>
>        Melting Tm: minimum Tm is <35>  maximum Tm is <95>
> Importing </home/user/exp/ann/miRNA-1_0_annot.csv> as <miRNA-1_0.ann>...
> Error: wrong token number for <>
> Error when reading file </home/user/exp/ann/miRNA-1_0_annot.csv>.
> Errore in import.expr.scheme("Scheme_miRNA_1_0", filedir = scmdir,
> paste(libdir,  :
>    error in function ‘ImportExprSchemes’
>
> I think that mirna_probe or annotation files from affymetrix aren't in
> the correct format or somewhat is missing probably.
>
>
> Thanks.
>
>
> Best regards.
>
> Giacomo
>
>
> down here my code:
>
> libdir <- "/home/user/exp/lib"
> scmdir <- "/home/user/exp/scheme"
> anndir <- "/home/user/exp/ann"
> scheme.mirna <- import.expr.scheme("Scheme_miRNA_1_0",filedir=scmdir,
> paste(libdir,"miRNA-1_0.CDF",sep="/"),paste(libdir,"miRNA-1_0.probe.tab",sep="/"),annotfile=paste(anndir,"miRNA-1_0.annot.csv",sep="/"))
>
>
>