[BioC] Questions about Limma package

[James W. MacDonald]

Hi Priscila,

Please don't respond just to me - we archive the questions and responses 
so other people can find answers to their questions.

Priscila Grynberg wrote:
> Hi Jim,
> I'll answer all your questions! Thanks!
> 
> 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".

This just means that you didn't have a carriage return after the last 
line of your targets file. If I take this and add a return, I get the 
following:

 > readTargets("tmp.txt")
           SlideNumber.FileName.Cy3.Cy5.Date
1 81 swirl.1.spot swirl wild type 2001/9/20
2 82 swirl.2.spot wild type swirl 2001/9/20
3 93 swirl.3.spot swirl wild type 2001/11/8
4 94 swirl.4.spot wild type swirl 2001/11/8

> 
> 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".

Same thing - just add a return at the end of the last line.

> 
> 
> 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?

You might want to upgrade to R-2.8.0 patched and BioC 2.3.

And let us know if you have any other problems.

Best,

Jim


> 
> 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
> 
> 

-- 
James W. MacDonald, M.S.
Biostatistician
Hildebrandt Lab
8220D MSRB III
1150 W. Medical Center Drive
Ann Arbor MI 48109-0646
734-936-8662