[BioC] Exact structure of RGList object (limma)

Gordon K Smyth smyth at wehi.EDU.AU
Tue Jun 21 12:25:10 CEST 2005

> Date: Mon, 20 Jun 2005 19:19:09 +0000
> From: "Ken Termiso" <jerk_alert at hotmail.com>
> Subject: [BioC] Exact structure of RGList object (limma)
> To: bioconductor at stat.math.ethz.ch
> Hi all,
> I am trying to take data from a scanner that is not part of the "core" group
> supported by limma, and create an RGList object from it, using the minimal
> components as defined in the limma docs. I've read in the CSV file and
> isolated the green and red F/G and B/G data for each chip, but what is
> unclear in the docs is the format that they need to be in...

Have you investigated using the 'columns' argument of the read.maimages() function?  See page 10
of the User's Guide for an example.  If your scanner outputs a CSV file for each array, it is
highly likely that you can simply set 'columns' and 'sep=","', and everything will work as for a
"core" scanner, with no need for you to assemble data structures for yourself.

> In other words, is the order of slots/list components in the RGList object
> R1, G1, Rb1, Gb1...R1n, G1n, Rbn, Gbn for each chip, or is it R1...Rn,
> G1...Gn, Rb1...Rn, Gb1...Gbn (where n is the number of chips)?

Type help("RGList-class") to see the definition of the structure of an RGList object.


> Thanks in advance,
> Ken

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