Dear Som,

I'm bringing this message back to the mailing list so it can be used as
reference for others.

COUNT is the number of features... You don't need to worry about this, just
make it 1.

Once you have the XYS files, you should use the pdInfoBuilder vignette.

b

On Mon, Mar 1, 2010 at 8:55 PM, somnath bandyopadhyay <
genome1976@hotmail.com> wrote:

>  Thanks for the info. What is the COUNT column?
>
> These are the columns in my *.pair files:
>
>
> IMAGE_ID GENE_EXPR_OPTION SEQ_ID PROBE_ID POSITION X Y MATCH_INDEX SEQ_URL PM MM
>
> Thanks,
> Som.
>    MATCH_INDEX SEQ_URL PM MM
>  > From: beniltoncarvalho@gmail.com
> > Date: Mon, 1 Mar 2010 20:39:47 +0000
> > Subject: Re: [BioC] makePDpackage
>
> > To: genome1976@hotmail.com
> > CC: bioconductor@stat.math.ethz.ch
> >
> > 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@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.
> > >
> > > _________________________________________________________________
> > > Hotmail: Trusted email with powerful SPAM protection.
> > >
> > >        [[alternative HTML version deleted]]
> > >
> > > _______________________________________________
> > > Bioconductor mailing list
> > > Bioconductor@stat.math.ethz.ch
> > > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > > Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
> > >
>
> ------------------------------
> Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. Sign up
> now. <http://clk.atdmt.com/GBL/go/201469229/direct/01/>
>

	[[alternative HTML version deleted]]

