[BioC] RinGO problem

[Jianping Jin]

Hi Joern,

There are 6247 probes with LENGTH <= 0 (actually <= -50). The minus sign 
may refer to the genome strain. I checked the demo data set which also 
contains minus values for LENGTH.

The only difference I can tell is the format of PROBE_ID. In the demo file 
it is something beginning with MM, e.g. MM5000P01479955, while in my file 
it is something like 5313_0514_0052.

Jianping

--On Monday, January 12, 2009 6:46 PM +0000 Joern Toedling 
<toedling at ebi.ac.uk> wrote:

> Hello,
>
> well, the culprit(s) is/are the matches with a negative entry in LENGTH,
> as these are not supposed to happen. I am not sure how these came about,
> but it might have to do with changes in Exonerate (the scripts were
> written for Exonerate version 2.0.0).  I shall investigate this further
> and get back to you. But for the moment, I am afraid you will have
> either to discard these lines with negative length matches before
> calling posToProbeAnno (how many are these?) or find a way to correct
> them in the Exonerate output file.
>
> Regards,
> Joern
>
> Jianping Jin wrote:
>> 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
>
> --
> 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