[BioC] Loading Niblegen Files to Oligo

[Benilton Carvalho]

The best thing to do is to go back to NimbleScan and generate the
reports using the XYS format. b

On 22 October 2010 23:56, Colleen Doherty <cdoherty at ucsd.edu> wrote:
> 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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