[BioC] Loading ArrayVision microarray data into Limma

[Gordon K Smyth]

Dear Maite,

Well, it's pretty hard to provide support for file formats that change or 
aren't documented.

The column headings in your file are not the same as the column headings 
in ArrayVision files that people have sent me in the past, and a google 
search doesn't find any documentation about what an ArrayVision file 
should contain.

Your file seems to have multiple columns with the same column heading 
(Dens and Bkgd both occur twice).  This makes the file pretty inscrutable, 
and pretty hard to read correctly using any software.  Your email is hard 
to read, with different rows from the files just run together. I wonder 
whether this is correct output from ArrayVision, or whether the file has 
been edited in some way.  It would seem that the file or your email 
description of it is in error.

Best wishes
Gordon

> Date: Sun, 24 Jun 2012 15:01:21 +0200
> From: Maite Iriondo <maiteiriondo at gmail.com>
> To: bioconductor at r-project.org
> Subject: [BioC] Loading ArrayVision microarray data into Limma
>
> 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
>

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