[BioC] makePDpackage

[Benilton Carvalho]

Hi Som,

use the pdInfoBuilder package instead.

About PAIR -> XYS... you need to create a text file with the following
columns (X/Y/SIGNAL/COUNT). It should be sorted by X and Y coordinates
and control probes should have NA in the SIGNAL column. All X/Y
coordinates should be included.

X  Y  SIGNAL  COUNT
1   1   321.12   1
1   2         NA   1
1   3    123.34  1
..  ..     .....

The XYS files can be generated directly from NimbleScan....

b

On Mon, Mar 1, 2010 at 8:27 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?
>
>
>
> Thank so much,
>
> Som.
>
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