[BioC] RinGO problem

[Jianping Jin]

Hi Joern,

Please see below,

--On Monday, January 12, 2009 5:44 PM +0000 Joern Toedling 
<toedling at ebi.ac.uk> wrote:

> Hi Jianping,
>
> I am not completely sure what the source of the error is yet, so bear
> with me as I am trying to find out.
> First, something could be wrong with the merged Exonerate output file.
> Which version of Exonerate are you using?

exonerate-2.2.0-x86_64
>
> Can you also please tell me what the output of
>
> summary(allchranno$LENGTH)

> summary(allchranno$LENGTH)
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max.
 -72.00   50.00   50.00   50.13   51.00   75.00

>
> and
>
> summary(allchranno$POSITION)

> summary(allchranno$POSITION)
     Min.   1st Qu.    Median      Mean   3rd Qu.      Max.
   133400  37680000  75400000  77490000 112700000 197100000
>
> are? Another issue could be the use of factors for probe and chromosome
> identifiers. When reading in the output file using read.table,
> read.delim etc., please try the argument "as.is=TRUE", which will
> prevent the conversion of character vectors into factors. You can then
> directly supply the data.frame allchranno to the function posToProbeAnno.
>
> probeAnno <- posToProbeAnno(allchranno)
>
> Please tell me whether the error message still persists. If so could you
> please provide me with the file allChromExonerateOut_scott.txt
> or an excerpt thereof (please do not attach it to the mail but provide
> it for download on some server) such that I can further look into the
> issue.
>
Yes. The problem is the same.

I put up the data file on <http://seattle.med.unc.edu/jjin/>. You can check 
that out.

Thanks,

Jianping

> Best regards,
> Joern
>
> Jianping Jin wrote:
>> 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_sc
>> ott.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
>>
>
> --
> Joern Toedling
> EMBL - European Bioinformatics Institute
> Wellcome Trust Genome Campus
> Hinxton, Cambridge CB10 1SD
> United Kingdom
> Phone  +44(0)1223 492566
> Email  toedling at ebi.ac.uk
>



##################################
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