[BioC] RMA Normalization Nimblegen with adf.txt file

[Federico Lasa]

Hr Piet,

I'm not familiar with adf file format but one thing you can do if you
have the raw .xys files is search for the paricular platform in GEO
and download the corresponding design (ndf) file from there, for
instance:

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL17894

has downloads for a particular vitis vinifera nimblegen expression
design (NimbleGen 090918 Vitus vinifera exp HX12). If that's not the
one you want, you'll probably find it there somewhere. Good Luck.

On Tue, Jul 1, 2014 at 2:58 PM, Piet Jones <pietjones at gmail.com> wrote:
> Hi,
>
> I am trying to normalize a nimblegen vitis vinifera microarray
> experiment. The normal procedure I use is to use the pdInfoBuilder
> package to create a R package from a xys file and a ndf file, I then
> install and load the package followed by using the read.xysfiles, rma
> and write.exprs methods in the oligo package.
>
> My problem is that the particular experiment I need to analyse only
> has a adf.txt file, I have searched in vain to find a way to convert
> this to ndf. Does anyone know of a way to do this? Or is there some
> alternative RMA normalization that can be done with nimblegen xys/pair
> files and a adf.txt file?
>
> Kind Regards,
> Piet Jones
>
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