[BioC] read.maimages in limma package

Giusy Della Gatta Gatta at icg.cpmc.columbia.edu
Wed Dec 17 14:24:38 CET 2008

Thank you Peter,

I'll check it out!
I have also seen that I have to make a file
in which I have to describe agilent 
annotations (see point 3 of my previuos email).

May you know where I have to check to retrieve 
informations on the file format that I have to use?

Thank you 

-----Original Message-----
From: john seers (IFR) [mailto:john.seers at bbsrc.ac.uk]
Sent: Wed 12/17/2008 4:36 AM
To: Giusy Della Gatta; bioconductor at stat.math.ethz.ch
Subject: RE: [BioC] read.maimages in limma package
Hi Giusy

If you look at the code for read.maimages you can see which columns
limma is expecting for agilent:

agilent = list(G = "gMeanSignal", 
            Gb = "gBGMedianSignal", R = "rMeanSignal", Rb =

If your custom arrays do not match these names then you have to specify
them yourself (using the columns parameter of read.maimages).


John Seers


I am analyzing custom two color agilent array by using limma package and
I am having some problems with the read.maimages

I launch this comand:

> read.maimages("Targets$Filename, source="agilent")

and the error that I have is the following:

Read Control_2b.txt
Read Control_3b.txt
Error in readGenericHeader(fullname, columns = columns) :
Specified column headings not found in file

It is like the columns in the file that I gave as input (Control_.txt)
are not recognized,
maybe I have this problem because is a custom agilent array?

If this is the problem, I have to specify in my script the following

1. list with fields R, G, Rb and Gb giving the column names to be used
for red and green foreground and background;
2. character vector of names of other columns to be read containing
spot-specific information;
3. character vector of names of columns containing annotation
information about the probes;

Is there someone that can answer me and that has got some experience in
two color agilent custom array analysis?

Thank you in advance

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