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

[cstrato]

Dear Giacomo,

Please use only the cdf and probe.tab files to create the scheme for 
miRNA. The reason is that the miRNA annotation does not follow the usual 
Affymetrix format for annotation files and thus can currently not be 
used to create the scheme file.
You need to import the annotation file directly into R using read.csv().

Best regards
Christian
_._._._._._._._._._._._._._._._._._
C.h.r.i.s.t.i.a.n   S.t.r.a.t.o.w.a
V.i.e.n.n.a           A.u.s.t.r.i.a
e.m.a.i.l:        cstrato at aon.at
_._._._._._._._._._._._._._._._._._



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="/"))
>
>
>