[BioC] RinGO problem

[Joern Toedling]

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?

Can you also please tell me what the output of

summary(allchranno$LENGTH)

and

summary(allchranno$POSITION)

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.

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_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
>

-- 
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