RMA Normalization Nimblegen with adf.txt file
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Piet Jones ▴ 30
@piet-jones-5574
Last seen 8.1 years ago
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
Normalization Vitis vinifera oligo Normalization Vitis vinifera oligo • 1.1k views
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@federico-lasa-6147
Last seen 8.1 years ago
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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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