[BioC] pdInfoBuilder for Niblegen 12x135k array, argument "posFile" is missing, with no default

[Benilton Carvalho]

The current version of the pdInfoBuilder package is 1.10.0.

So, my first recommendation is to upgrade your R installation to the
latest available version, so you can use the aforementioned
pdInfoBuilder package.

Once that's done, I'd suggest you to try the script again and I'll be
able to help you out.

Cheers,

b

On Fri, Feb 5, 2010 at 1:52 PM, Chris Fenton <chrisf at fagmed.uit.no> wrote:
> Pretty much copied the code from
> http://linusben.net/wiki/index.php/Oligo.bioconductor.
>
>
> Something ala,
>
> """
>> library(pdInfoBuilder)
>> filename_ndf <- list.files('.',pattern='.ndf',full.names=T)
>> filename_xys <- list.files('.',pattern=".xys",full.names=T)[1]
>> seed <- new("NgsExpressionPDInfoPkgSeed", ndfFile=filename_ndf, xysFile=filename_xys,
>            author="Taejoon Kwon",email="email address",
>            biocViews="AnnotationData", genomebuild="Unknown",
>            url="http://www.marcottelab.org")
>> makePdInfoPackage(seed, destDir = ".")
> """
>
> I get the folling error in the seed <- new(...) line
>
> """
> argument "posFile" is missing, with no default
> """
>
>
> Can't seem to find any documentation on this parameter.
> Anyone run into this ?
>
> Chris
>
>
>
> sessionInfo()
>
> R version 2.7.2 (2008-08-25)
> i686-pc-linux-gnu
>
> locale:
> C
>
> attached base packages:
> [1] splines   tools     stats     graphics  grDevices utils     datasets
> [8] methods   base
>
> other attached packages:
> [1] pdInfoBuilder_1.4.0  oligo_1.4.0          oligoClasses_1.2.0
> [4] AnnotationDbi_1.2.2  preprocessCore_1.2.1 affxparser_1.12.2
> [7] RSQLite_0.7-1        DBI_0.2-4            Biobase_2.0.1
>
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