It ended up being a simple problem of data.frame manipulation. The following works it out:rownames(targets) <- targets[,1] Cheers, Massimo On Thu, May 7, 2009 at 4:17 PM, Massimo Pinto <pintarello@gmail.com> wrote: > thank you...getting worse though. > X FileName Treatment FileName2 Biorep Culture > Array targets$FileName > 41741_1_1_1 41741_1_1_1 41741_1_1_1.txt Cn 1 1 t0 > 41741 41741_1_1_1.txt > 41742_1_1_3 41742_1_1_3 41742_1_1_3.txt Cn 1 3 t0 > 41742 41742_1_1_3.txt > 41744_1_4_4 41744_1_4_4 41744_1_4_4.txt Cn 1 4 t0 > 41744 41744_1_4_4.txt > > Anyways I should be able to tweek it with your hints, now! Fingers crossed. > Cheers > Massimo > > On Thu, May 7, 2009 at 3:58 PM, Pedro Lopez-Romero < > plromero1.bioc@gmail.com> wrote: > >> Hi Massimo, >> >> just try >> >> > targets=cbind(targets,targets$FileName) >> > targets[,1]=rownames(targets) >> > colnames(targets)[4]='FileName2' >> > targets >> >> p.- >> >> On Thu, May 7, 2009 at 9:31 AM, Massimo Pinto <pintarello@gmail.com>wrote: >> >>> Greetings all, >>> please consider my targets file >>> >>> FileName Treatment GErep Biorep Culture Array >>> t0Cn1 41741_1_1_1.txt Cn 1 1 t0 41741 >>> t0Cn3 41742_1_1_3.txt Cn 1 3 t0 41742 >>> .... >>> >>> how can I make read.targets() use my first targets column to define the >>> row >>> names, and make them available (as t0Cn1, toCn3 instead >>> of 41741_1_1_1, 41742_1_1_3) for all plotting functions that are supplied >>> in >>> the Agi4x44PreProcess package? It would help extract sense from all of >>> those >>> plots. >>> As an alternative, I may re-define the filenames, but it kind of make >>> sense >>> to retain their original names. Plus, it would be a declararion of >>> defeat. >>> >>> Inspired by the help file for read.targets(), I am trying to borrow the >>> argument row.names from the function read.data() >>> >>> > targets=read.targets(infile="Targets_T0.txt", row.names=1) >>> to no avail, as I may be forcing read.targets() to work like read.data, >>> while the two functions may not know each other. >>> >>> row.namesa vector of row names. This can be a vector giving the actual >>> row >>> names, or a single number giving the column of the table which contains >>> the >>> row names, or character string giving the name of the table column >>> containing the row names. >>> If there is a header and the first row contains one fewer field than the >>> number of columns, the first column in the input is used for the row >>> names. >>> Otherwise if row.names is missing, the rows are numbered. >>> Using row.names = NULL forces row numbering. Missing or NULL row.names >>> generate >>> row names that are considered to be ‘automatic’ (and not preserved by >>> >>> as.matrix<file: library="" frameworks="" r.framework="" resources="" library="" base="" html="" matrix.html=""> >>> ). >>> >>> thank you >>> Massimo >>> >>> -- >>> Massimo Pinto >>> Post Doctoral Research Fellow >>> Enrico Fermi Centre and Italian Public Health Research Institute (ISS), >>> Rome >>> http://claimid.com/massimopinto >>> >>> [[alternative HTML version deleted]] >>> >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor@stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> >> > > > -- > Massimo Pinto > Post Doctoral Research Fellow > Enrico Fermi Centre and Italian Public Health Research Institute (ISS), > Rome > http://claimid.com/massimopinto > -- Massimo Pinto Post Doctoral Research Fellow Enrico Fermi Centre and Italian Public Health Research Institute (ISS), Rome http://claimid.com/massimopinto [[alternative HTML version deleted]]