[BioC] affy to normalize others single chanels...

[Gordon K Smyth]

> Date: Wed, 05 Jan 2005 10:47:32 -0800
> From: Wolfgang Huber <huber at ebi.ac.uk>
> Subject: Re: [BioC] affy to normalize others single chanels...
> To: Marcelo Luiz de Laia <mlaia at fcav.unesp.br>
> Cc: bioconductor at stat.math.ethz.ch
> Message-ID: <41DC3644.5040305 at 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