[BioC] RinGO problem

[Jianping Jin]

Dear list,

I ran "runExonerate.sh" and had the per-chromosome output files condensed 
into one single file (see below,
I read in the file just for viewing):

> str(allchranno)
'data.frame':   390388 obs. of  6 variables:
 $ SEQ_ID    : Factor w/ 388250 levels "chr1:10000013-10000070",..: 31687 
28404 33240 34681 29011 26915 ...
 $ PROBE_ID  : Factor w/ 373478 levels "5313_0001_0001",..: 138251 325230 
15265 268671 45500 270116  ...
 $ CHROMOSOME: Factor w/ 21 levels "1","10","11",..: 2 2 2 2 2 2 2 2 2 2 ...
 $ POSITION  : int  75573476 4540877 79390517 80647222 5734395 30338873 
82085749 7386228 61247293 ...
 $ LENGTH    : int  50 50 50 60 50 60 50 50 50 52 ...
 $ MISMATCHES: int  0 0 0 0 0 0 0 0 0 0 ...

But when I tried to map probes to the genome I got an error and warnings:

probeAnno <- 
posToProbeAnno("C:/from_DriveD/Chip-chip/Bultman/allChromExonerateOut_scott.txt")
Creating probeAnno mapping for chromosome 1 10 11 12 13 14 15 16 17 18 19 2 
3 4 5 6 7 8 9 X Y Done.
Error in validObject(.Object) : invalid class "probeAnno" object: FALSE
In addition: Warning message:
In validityMethod(object) :
  Some match positions end before they actually start.
Please check elements 1.start and 1.end .

Appreciate it if you can help!

Jianping

FYI:

> sessionInfo()
R version 2.8.0 (2008-10-20)
i386-pc-mingw32

locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United 
States.1252;LC_MONETARY=English_United 
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

attached base packages:
[1] splines   tools     stats     graphics  grDevices utils     datasets 
methods   base

other attached packages:
 [1] Ringo_1.6.0         SparseM_0.78        RColorBrewer_1.0-2  vsn_3.8.0 
affy_1.20.0
 [6] limma_2.16.3        geneplotter_1.20.0  annotate_1.20.1 
xtable_1.5-4        AnnotationDbi_1.4.2
[11] lattice_0.17-15     genefilter_1.22.0   survival_2.34-1 
Biobase_2.2.1

loaded via a namespace (and not attached):
[1] affyio_1.10.1        DBI_0.2-4            grid_2.8.0 
KernSmooth_2.22-22   preprocessCore_1.4.0
[6] RSQLite_0.7-1

##################################
Jianping Jin Ph.D.
Bioinformatics scientist
Center for Bioinformatics
Room 3133 Bioinformatics building
CB# 7104
University of Chapel Hill
Chapel Hill, NC 27599
Phone: (919)843-6105
FAX:   (919)843-3103
E-Mail: jjin at email.unc.edu