[BioC] XYS from nimblegen

[Marcelo Brandão]

Hello there.
Does anyone knows how to generate XYS file from nimblegen pair file?
I am having a lot of problem trying to do accomplish this and analyze
my data thru bioconductor.
I have two main errors.
One if I try to read xys file a receive this:
> dat <- read.xysfiles(xys_files)
Platform design info loaded.
Checking designs for each XYS file... Done.
Allocating memory... Error in smartReadXYS(filenames, sampleNames) :
  negative extents to matrix
OR
When i am building annotation package:

> makePdInfoPackage(seed, destDir = ".")
================================================================================
Building annotation package for Nimblegen Expression Array
NDF: 2006-08-18_TI4932_60mer.ndf
XYS: 50186202_532.xys
================================================================================
Parsing file: 2006-08-18_TI4932_60mer.ndf... OK
Parsing file: 50186202_532.xys... OK
Merging NDF and XYS files... OK
Preparing contents for featureSet table... OK
Preparing contents for bgfeature table... OK
Preparing contents for pmfeature table... OK
Error in parseNgsPair(object at ndfFile, object at xysFile, verbose = !quiet) :
  Control probe possibly identified as Experimental


I know, I Know, this seems to be easy, but I can not understand what
is going on!!!

Thanks in advance for all of list members for your time reading this.

My best regards

Marcelo


-- 
Marcelo Mendes Brandão
Postdoc fellow
Laboratório de Biologia Molecular de Plantas - ESALQ/USP
Website: http://bioinfo.esalq.usp.br
AtPIN: http://bioinfo.esalq.usp.br/atpin
SKYPE: mmbrand
Tel: (+55) 19 3429 4442