I received an email with a few questions to help you to understand my
difficulties. I answered them:


1) What does your targets.txt file look like?

-  Well, I tried two different formats. The first one was based on a model
that I already have:

SlideNumber FileName Cy3 Cy5 Date
81 swirl.1.spot swirl wild type 2001/9/20
82 swirl.2.spot wild type swirl 2001/9/20
93 swirl.3.spot swirl wild type 2001/11/8
94 swirl.4.spot wild type swirl 2001/11/8

But instead of filename.spot, I wrote my filenames.gpr. But it didn't work.
I used the command
targets <- readTargets ("Targets.txt") following Limma userguide manual. I
receive this error message:

In read.table(file, header = TRUE, as.is = TRUE, sep = sep, quote = quote,
 :
  linha final incompleta encontrada por readTableHeader em 'Targets.txt' =
incomplete final line found by readTableHeader in "Targets.txt".

Then I tried to create a file just like the userguide suggests: "We assume
that the images have been analyzed using GenePix to produce a .gpr fi le for
each array and that a targets fi le targets.txt has been prepared with a
column containing the names of the .gpr fi les."

Then, my Targest.txt file looked like that:

Controle_Cy3x0horas_Cy5.gpr
0horas_Cy3xControle_Cy5.gpr

I received the same message. The next step was to create a column name
(FileName), and I changed the command line:

readTargets(file="Targetsb.txt", path=NULL, sep="\t"). This was the message
that I received:
                     FileName
1 Controle_Cy3x0horas_Cy5.gpr
2 0horas_Cy3xControle_Cy5.gpr
Warning message:
In read.table(file, header = TRUE, as.is = TRUE, sep = sep, quote = quote,
 :
  linha final incompleta encontrada por readTableHeader em 'Targetsb.txt'
= = incomplete final line found by readTableHeader in "Targets.txt".


2) What sort of microarray data are you analyzing?

I'm analysing an oligo slide. The experiments are dye-swap (two-channels).

3) what do you get when you submit sessionInfo() at an R prompt?

R version 2.7.2 (2008-08-25)
i386-pc-mingw32

locale:
LC_COLLATE=Portuguese_Brazil.1252;LC_CTYPE=Portuguese_Brazil.1252;LC_MONETARY=Portuguese_Brazil.1252;LC_NUMERIC=C;LC_TIME=Portuguese_Brazil.1252

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] limma_2.14.7


Thanks so much!

Priscila

-- 
Priscila Grynberg, B.Sc., M.Sc.
Doutoranda em Bioinformática (Bioinformatics D.Sc student)
Laboratório de Genética Bioquímica
Universidade Federal de Minas Gerais
Tel: +55 31 3409-2628
CV: http://lattes.cnpq.br/8808643075395963

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