[BioC] limma

[James Wettenhall]

Hi Peter,

The source code of limma is certainly available, at:
http://bioinf.wehi.edu.au/limma/limma_1.7.2.tar.gz

You can unzip and untar the package with:

tar zxvf limma_1.7.2.tar.gz

or

gunzip limma_1.7.2.tar.gz
tar xvf limma_1.7.2.tar


If you are using Windows, you can obtain tar and gunzip from
the Rtools bundle at:
http://www.murdoch-sutherland.com/Rtools/

(Or you may be able to unzip a tarball with Winzip, but I'd
recommend using tar and gunzip.)

If you are using Mac, tar and gunzip should be available in the
apple developer tools.

Hopefully you realize that normalizeWithinArrays can already
accept weights, so you can give some spots zero weight if you
want, then exclude them completely after normalization.

One comment about typing the name of an R function and pressing
enter is that sometimes (especially on Windows) if the source
code of the function contains an escpaed character like a tab:
sep="\t"
it may be displayed as:
sep="	"
when you type the function name and press enter within R.

For an example of this, try typing the name of the limma
function read.maimages and pressing Enter, then scroll back up
and look at the 'sep' argument.

Regards,
James