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Dear Chintanu, the target file can be (needs to be) produced by you, it is a way of telling the various subsequent analysis methods which biological samples were on which array, which colour etc. Regarding installation, please do follow the instructions at http://www.bioconductor.org/download Best wishes Wolfgang ------------------------------------------------------------------ Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber Chintanu scripsit: > Hi All, > > I'm a novice both to R and microarray, and am struggling to learn both by > myself. Currently, I have got a microarray dataset from a research lab > which contains cDNA and Affymetrix data files. The R-based literature refers > many times to a file that contains target description (a .txt file with > names like target.txt). But my dataset interestingly doesn't have any of > such files. I am now struggling to find out how important this .txt file is > as otherwise I have all the relevant image processing output files (e.g., > .gpr file). From the literature, I do understand that the so-called 'target > file' contains information about the RNA samples used as targets in the > microarray experiment, yet I'm wondering whether such files may be created > at one's end too. Or, is it ONLY the relevant lab which can give me this > file and else I can't move ahead! > > > > However, I do see that there is an information file in the dataset which > talks about the patient's name, file name and so on, but somehow I am > pessimistic that this is the file I am looking for (a part of it is attached > below). > > > > Patients File Cy5 Cy3 > Gal_File > GenePix Notes > > PreB1 B1a Test Control Pool > HS_10.5K_GP.gal > Pro 3.0 > > B1b Test Control Pool > HS_10.5K_GP.gal Pro 3.0 > > B1cDS Control Pool Test > HS_10.5K_GP.gal Pro 3.0 Dye Swap > > PreB2 B2a Test Control Pool > HS_10.5K_GP.gal > Pro 3.0 > > B2b Test Control Pool > PMCI_10.5KSC_GP.gal Pro 3.0 > > B2cDS Control Pool Test > HS_10.5K_GP.gal Pro 3.0 Dye Swap > > > > > *Part 2*: > > I'm also struggling to figure out why I get error messages, as below, while > loading certain packages and whether there is a way to correct this problem > . > > > library(marrayPlots) > Error in library(marrayPlots) : > 'marrayPlots' is not a valid package -- installed < 2.0.0? > > > > library(marrayNorm) > Error in library(marrayNorm) : > 'marrayNorm' is not a valid package -- installed < 2.0.0? > > > May I request you to kindly reply and help me out, please ! > > Cheers, > > Chintanu > > [[alternative HTML version deleted]]