[BioC] background correction

[Ben Bolstad]

Pedro,

You can use the the rma background correction and normalization routines
on a matrix. bg.adjust() implements basically the same background
correction functionality that is carried out by the rma() command
(except that rma() is implemented in compiled code).

The easiest way for you to do this would be


my.matrix.bg.rma <- apply(my.matrix, 2, bg.adjust)

my.matrix.norm <- normalize.quantiles(my.matrix.bg.rma)


Ben






On Mon, 2006-02-20 at 15:23 +0100, Pedro López Romero wrote:
> Hi all,
> 
> 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 Im not sure if
> I can apply this function directly to my data (a matrix with just raw
> foreground intensities).
> 
> Ive read the help file of this function but I still have some doubts. I
> have understood that  bg.adjust ( ) is the internal function that uses rma
> ( )  to correct for the background bias. I figure that the input that it
> needs is just a matrix with the raw intensities in natural scale and from
> here, the function estimates the signal intensities corrected by the
> background without using the background measures at all. Am I right?. My
> data does not have PM and MM intensities, all  the values are PM  and I
> have a probe per gene, Would still it be correct under theses cirmcumstances
> using the bg.adjust ( ) function?
> 
> 
> Other authors suggest to estimate the true signal intensities  just by
> substracting the median of the background probe intensities from the mean of
> the foreground ones, and setting the negative values, lets say 0.5. I think
> that this method is not completely correct, whats your opinion about
> this?.-
> 
> Moreover, I want to use the quantiles method to normalize the same data,
> would it be right to apply the normalize.quantiles ( ) function directly to
> the previous background corrected matrix?-
> 
> Thanks a lot.-
> 
> Pedro
> 
> 
> 
> 
> 
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