[BioC] Loading Niblegen Files to Oligo

Colleen Doherty cdoherty at ucsd.edu
Sat Oct 23 00:56:23 CEST 2010

 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:
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
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!

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

[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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