[BioC] help

James Wettenhall wettenhall at wehi.edu.au
Mon Jul 12 12:30:22 CEST 2004

Hi Michael,

On Fri, 9 Jul 2004, Michael Stapelberg wrote:
> A.object<-maA(objectscalenormalisation)
> M.object<-maM(objectscalenormalisation)

You really need to explain what you did from the beginning.  The
R commands you have presented begin with the functions maA() and
maM().  If they are from the "marray" package then you should
say that explicitly, i.e. you should say that you used:


> a<-is.na(M.object)

If you are worried about background-corrected red or green
intensities being negative and log ratios then being undefined
or in other words Not Available (NA), then this "problem" is
certainly not unique to your data set.  The authors of the
marray and limma packages are well aware of this issue and
there are automatic methods to deal with this.  You shouldn't
need to manually check for NAs for every data set.

I would suggest going through the examples in the limma and
marray documentation, and trying to apply the steps to your data
set as closely as possible.  If you are using limma, you will
create an MAList object (the usual name given to this object is
"MA").  If you are using the marray package, you will instead
create an marrayNorm object (which contains M and A objects
after normalization, within an S4 object).

You seem to be creating M and A using a non-standard method (or
extracting them from an marrayNorm object unnecessarily), so
this makes it difficult for people to help you.  If you want to
convert an marrayNorm object (from the marray package) into an
MAList object (for the limma package), in order to fit a linear
model, there are automatic coercion (conversion) functions to do
this in the convert pacakge, i.e. you don't need to extract M
and A manually.

To convert an marrayNorm object to an MAList object, you can do:

mnorm <- new("marrayNorm")
MA <- as(mnorm,"MAList")

Replace "mnorm" above with your object of class marrayNorm.


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