[BioC] background correction

[Pedro López Romero]

Hi Georg,
I am not using the rma( ) directly but the bg.adjust ( ) function, which I
think it is the internal function that rma ( ) uses.- I thought that this
function could be applied directly to a matrix of raw intensities without
worring too much about whether we have multiple probes per gene or not. I
might be misunderstood, though.-

I will have a look at the limma package as well.-

Thanks a lot.

Best whishes

p.-



-----Mensaje original-----
De: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch]En nombre de Georg Otto
Enviado el: martes, 21 de febrero de 2006 11:01
Para: bioconductor at stat.math.ethz.ch
Asunto: Re: [BioC] background correction

Pedro López Romero <plopez at cnic.es> writes:

Pedro,

>
> I want to normalize some data comming from a single chanel non affy
> platform.- Id like to use the rma( ) function, but I would need to create
> first an Affybatch object from the data that I have, a task that I find a
> bit difficult to do given the data that I have. I think that would be much
> more easier to use the bg.adjust ( ) internal function, but I m not sure
if
> I can apply this function directly to my data (a matrix with just raw
> foreground intensities).
>

you can not use RMA for your data, since it is designed for Affymetrix
arrays, where you always multiple probes per gene.


You should have a look at the users guide of the package limma and at
the man pages of the functions described therein. You will find
several methods for background correction and normalisation. For single
channel data, you should have a look at chapter 9 of the limma users
guide.


Best,

Georg

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