[BioC] makePDpackage

Sean Davis seandavi at gmail.com
Mon Mar 1 21:38:18 CET 2010

On Mon, Mar 1, 2010 at 3:27 PM, somnath bandyopadhyay
<genome1976 at hotmail.com> wrote:
> Hi,
> I am trying to annotate the Nimblegen 385k mm8  refseq promoter chip and the following is what I have been using:
>> makePDpackage("2006-07-18_MM8_RefSeq_promoter.ndf", "FILE.XYS", "2006-07-18_MM8_RefSeq_promoter.pos",manufacturer="nimblegen", type="expression", genomebuild = "mm8")
> nimblegen expression
> The package will be called pd.2006.07.18.mm8.refseq.promoter
> Reading 2006-07-18_MM8_RefSeq_promoter.ndf
> Assuming a simple design (NOT multiple-wells).
> Correcting probe positions... Done.
> Error in getClass(Class, where = topenv(parent.frame())) :
>  "platformDesign" is not a defined class
> Could anybody help me out with this? Moreover, is there a way to convert .pair files into .XYS files for nimblegen?

Hi, Somnath.  It is always useful to include sessionInfo() output when
reporting errors.  Without this information, it is difficult to
determine what the problem might be.


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