[BioC] loading composite data (bg corrected) into limma

[Sean Davis]

On 5/24/06 6:06 AM, "Sharon" <sharonanandhi at gmail.com> wrote:

> Hi,
> 
> I am looking for a way to load background corrected data (all the 24 arrays
> in a single file) into limma. This is a 2-channel array data, so I have 3
> columns (cy3, cy5 & flag) for each array with probe name & ID.  I have tried
> to load the data with read.table(). Now, do I need to convert this table
> into RGList?

You need to make 3 separate matrices for cy3, cy5, and, if you want to use
flag, a "weights" matrix; all of this can be done by subsetting out the
columns that you want from your "big table".  Then you can construct your
RGList by hand.  You will of course probably want to add a "targets"
data.frame as well as gene information.  After that, everything should
proceed as normal. 

Sean