Hi Coleen
I just have the same problem. I wrote an perl script to produce tha xys file
using the pair files and the ngd file. I am now away from my lab, if you are
interested I may send it to you.
Cheers
Marcelo

——
Marcelo Mendes Brandão
http://bioinfo.esalq.usp.br
skype: mmbrand
via Android

Em out 22, 2010 8:57 PM, "Colleen Doherty" <cdoherty@ucsd.edu>escreveu:

Hello,
 We are trying to load Nimblegen Files to the Oligo Package.  We do
not have .xys files so tried to make them from the .pair files
following this link:
http://permalink.gmane.org/gmane.science.biology.informatics.conductor/29947
However, when trying to read them into Oligo we get this error

> 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

I guess we do not have the .xys files made correctly, but I'm not sure
what we have incorrect, since I can't find exactly what it should look
like.
This is what we have:

# software=NimbleScan   version=2.4.27 designname=090717_Athal_TAIR9_exp
X       Y       EOL     Count
23      3       731.67  NA
135     3       317.33  NA
137     3       742.44  NA
139     3       264.89  NA
141     3       2006.22 NA
143     3       898.11  NA

Does anyone see anything obvious we have wrong?
Session info is below
Any advice would be appreciated.
Thanks very much!
Colleen



> sessionInfo()
R version 2.12.0 (2010-10-15)
Platform: i386-apple-darwin9.8.0/i386 (32-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] pd.090717.athal.tair9.exp_0.0.1 RSQLite_0.9-2
[3] DBI_0.2-5                       oligo_1.14.0
[5] oligoClasses_1.12.0             Biobase_2.10.0

loaded via a namespace (and not attached):
[1] affxparser_1.22.0     affyio_1.18.0         Biostrings_2.18.0
[4] IRanges_1.8.0         preprocessCore_1.12.0 splines_2.12.0
>

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