[BioC] background correction

[Georg Otto]

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