[BioC] Normalizing data (that is not in microarray "format")

[Sean Davis]

On Fri, Dec 5, 2008 at 10:08 PM, Emmanuel Levy <emmanuel.levy at gmail.com> wrote:
> Dear All,
>
> I am trying to normalize data that looks like absolute mRNA expression
> values (although it's not).
> This means that I do not have an affy object.
>
> I' tried normalize.loess, which partially worked as it gave me the
> following warning (when I set missing values to 1 it disappears):
>
> 50: In means[, k] - aux ... :
>  longer object length is not a multiple of shorter object length
>
>
> I'd like to use other methods (linear or non linear), but I've got a
> problem because I do not have an expression object.
> --> for example,  maNorm doesn't work and I've got the following error:
>
> Error in slot(mnorm, "maNormCall") <- match.call() :
>  object "mnorm" not found
>
> Any idea on which functions to use, or on how to "transform" my
> data.frame into an affy object would be great.

Hi, Emmanuel.

Reading the help for normalize.loess, it appears that it takes a
matrix as input.  You do not need an affy object.  Also, note that a
data.frame is not a matrix.  For any of the normalization methods that
you might choose, it helps to read the help carefully, as that will
tell you what types of data can be used; most normalization routines
will take a matrix as input.  If you need more specific help, you will
need to post some reproducible example code and give the output of
sessionInfo().

Sean