Hello,

I have got .csv data from a*  Pseudomonas putida* microarray which was
analysed with ArrayVision image analysis software, in which the numbers (1,
2,..5) correspond to different times when the samples were taken and the
"c" stands for control.
I am using Limma to upload my data, however I get an error in which says
that the foreground columns for the file in which I store the intensities
are not found.
My data for the two-channel microarray was given in this format:

   AA30_1 AA30_1c  SpotNr SpotType Gene Dens Bkgd Dens Bkgd  Spot0001 A
korA2 224.16 110 491.68 235  Spot0002 A korA2 203.44 113 433.33 246.5
Spot0003 A mpfH 167.12 116 386.53 262.5  Spot0004 A mpfH 145.63 113 392.1
249  Spot0005 C DMSO 126.23 116 275.03 260.5  Spot0006 C DMSO 126.61 116
254.69 275.5
I defined the targets file:
targets<- readTargets(file="TargetsAA30.csv", sep=",")

 FileName Cy3 Cy5  AA301.csv AA30_1 AA30_1c  AA302.csv AA30_2 AA30_2c
AA303.csv AA30_3 AA30_3c  AA304.csv AA30_4 AA30_4c  AA305.csv AA30_5 AA30_5c

 and when reading the raw data I have the following error:

> RG<- read.maimages(targets$FileName, "arrayvision")
Error in read.maimages(targets$FileName, "arrayvision") :
  Cannot find foreground columns in AA301.csv

I would like to know if the structure of my initial file is correct for the
read.maimage function using source= "arrayvision", or if there is any
changes I can make in order to upload my data.
Thank you in advanced,

Maite Iriondo

	[[alternative HTML version deleted]]

