Hi eveyone, my name is Priscila, and I'm beginning to use Limma package to analyse my microarray data. Could someone help me? I can't even start to analyse my data because I can't read my file Targets.txt using the Limma package. I don't know which information this file must contains, except for the .gpr file. Does anyone have a model? Thanks! Priscila [[alternative HTML version deleted]]

Hi Priscila, I think we will need some more information before anybody will be able to help you. What does your targets.txt file look like? What sort of microarray data are you analyzing? What have you tried so far? Have you had errors, if so what did you do that caused the error to occur? Also, what do you get when you submit sessionInfo() at an R prompt? Best, Jim Priscila Grynberg wrote: > Hi eveyone, > > my name is Priscila, and I'm beginning to use Limma package to analyse my > microarray data. > > Could someone help me? I can't even start to analyse my data because I can't > read my file Targets.txt using the Limma package. I don't know which > information this file must contains, except for the .gpr file. Does anyone > have a model? > Thanks! > > Priscila > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Hildebrandt Lab 8220D MSRB III 1150 W. Medical Center Drive Ann Arbor MI 48109-5646 734-936-8662

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_Brazi l.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

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_M ONETARY=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 [[alternative HTML version deleted]]