[BioC] read.maimages in limma package

Giusy Della Gatta Gatta at icg.cpmc.columbia.edu
Wed Dec 17 06:34:10 CET 2008

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 informations:

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 the 
two color agilent custom array analysis?

Thank you in advance

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