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

[giacomo.tuana at unimib.it]

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="/"))


-- 

Dr. Giacomo Tuana Franguel

Genopolis Consortium
University of Milano-Bicocca
Dept. of Biotechnology and Bioscience/ U4
Piazza della Scienza 4 20126 Milano, Italy
Tel +39 02 6448 3530
Fax +39 02 6448 3550
http://www.genopolis.it
					
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