Hi Bioconductors, A happy new year to all! We have a raw data from naylon membrane (cDNA) and we would like to read and normalize it on affy package. Anyone do this (read and normalize) in affy package? Is it possible? Is a good idea? Thanks a lot Marcelo

Hi Marcelo, Marcelo Luiz de Laia wrote: > We have a raw data from naylon membrane (cDNA) and we would like to read > and normalize it on affy package. > > Anyone do this (read and normalize) in affy package? Is it possible? Is > a good idea? What I have been doing is to read them in simply with the function "read.table", collect the different arrays into a matrix, and then use the function "vsn" from the package of the same name to normalize the data. For comparison, you could also use normalize.quantiles from the affy package (it works on matrices). I don't think the "AffyBatch" class, which is the main data structure of the affy package, is terribly useful for nylon membrane data, since there are no probe sets. Consider just using the "exprSet" class instead. Also, with some tweaking the package "arrayMagic" provides functions that might be useful for data import, quality control and visualization of these data. Unfortunately the documentation largely ignores nylon membranes, and you will probably need to make some workarounds, so I'd only recommend this if you are fairly comfortable with R. Good luck with the filters! -- Best regards Wolfgang ------------------------------------- Wolfgang Huber European Bioinformatics Institute European Molecular Biology Laboratory Cambridge CB10 1SD England Phone: +44 1223 494642 Fax: +44 1223 494486 Http: www.ebi.ac.uk/huber

> Date: Wed, 05 Jan 2005 10:47:32 -0800 > From: Wolfgang Huber <huber@ebi.ac.uk> > Subject: Re: [BioC] affy to normalize others single chanels... > To: Marcelo Luiz de Laia <mlaia@fcav.unesp.br> > Cc: bioconductor@stat.math.ethz.ch > Message-ID: <41DC3644.5040305@ebi.ac.uk> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > Hi Marcelo, > > Marcelo Luiz de Laia wrote: >> We have a raw data from naylon membrane (cDNA) and we would like to read >> and normalize it on affy package. >> >> Anyone do this (read and normalize) in affy package? Is it possible? Is >> a good idea? > > What I have been doing is to read them in simply with the function > "read.table", collect the different arrays into a matrix, and then use > the function "vsn" from the package of the same name to normalize the > data. For comparison, you could also use normalize.quantiles from the > affy package (it works on matrices). normalizeQuantiles() in the limma package might also be useful because it allows for missing values while normalize.quantiles() doesn't. Gordon > I don't think the "AffyBatch" class, which is the main data structure of > the affy package, is terribly useful for nylon membrane data, since > there are no probe sets. Consider just using the "exprSet" class instead. > > Also, with some tweaking the package "arrayMagic" provides functions > that might be useful for data import, quality control and visualization > of these data. Unfortunately the documentation largely ignores nylon > membranes, and you will probably need to make some workarounds, so I'd > only recommend this if you are fairly comfortable with R. > > Good luck with the filters! > > -- > Best regards > Wolfgang > > ------------------------------------- > Wolfgang Huber > European Bioinformatics Institute > European Molecular Biology Laboratory > Cambridge CB10 1SD > England > Phone: +44 1223 494642 > Fax: +44 1223 494486 > Http: www.ebi.ac.uk/huber

i used normalize.quantiles on data from a similar platform and was satisfied with the results. give it try.. -r On Tue, 4 Jan 2005, Marcelo Luiz de Laia wrote: > Hi Bioconductors, > > A happy new year to all! > > We have a raw data from naylon membrane (cDNA) and we would like to read and > normalize it on affy package. > > Anyone do this (read and normalize) in affy package? Is it possible? Is a > good idea? > > Thanks a lot > > Marcelo > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >