[BioC] widget.marrayRaw

[Sandrine Dudoit]

Hi Niklas,


On Tue, 4 Jun 2002, Niklas Nordquist wrote:

> I have a couple of questions concerning the marrayRaw widget.
> First, when I create an marrayLayout object and specify a "*.gal" file
> containing info on spots and clones, and just type ">objectname", I get
> some summary information on the object. In this summary it is stated
> that I have a number of control spots, including 3xSSC, the Arab gene,
> and duplicates of each spot. Where does this information come from?

This information was stored in your .gal file.

Once you select an Info file (say myfile.gal) in the marrayLayout widget
and click on GetInfo, a new widget opens up asking you to select the
column which holds the control information in myfile.gal. You must have
selected one of the myfile.gal columns when reading the data into R.

> Second, Is this information about control spots used in the
> normalization process? (I have used the maLormLoess() function).

It's used only if you tell the normalization function to do so. For
example, when using maNorm, the argument "subset" can be used to specify
which spots to use in the normalization.

Best,
Sandrine


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