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Then please supply the output of sessionInfo() and at least some of the input you used. How did you install the packages, please supply the commands you used, don't say: "I followed the instructions", that is too vague and presumes that you made no errors doing that. There are very many things that could go wrong, and you will need to provide a great deal more information before anyone could help you. Chintanu wrote: > Dear Wolfgang, > > Thanks for your reply ! > > Regarding the error-message, I have it even reinstalled (following the > instructions from Bioconductor webpage), but still getting no escape from > it. While searching on the web on it, I didn't get the solution but found > people mentioning about it: > > http://www.google.com/search?hl=en&q=%22is+not+a+valid+package+--+in stalled+%3C+2.0.0%3F%22&btnG=Search > > Cheers, > Chintanu > > = = = = = = = = = = = = = = = = = = > > > On Feb 9, 2008 1:00 AM, Wolfgang Huber <huber at="" ebi.ac.uk=""> wrote: > >> 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]] > > [[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 > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org

Hi Christina, It looks like you are trying to read in arrays with different print layout. What type of arrays are you using? Do they come from the same print? Best, Agnes ________________________________ From: bioconductor-bounces@stat.math.ethz.ch on behalf of Christina Tigress Sent: Thu 2/14/2008 6:31 PM To: Bioconductor at stat.math.ethz.ch Subject: [BioC] error message Hi Experts, While trying to analyse a few .gpr files, I'm come across the following message which I am unable to understand (confession: new to this area). The information's given below: > sessionInfo () R version 2.6.0 (2007-10-03) i386-pc-mingw32 locale: - -- -- - - - - attached base packages: [1] grid tools stats graphics grDevices datasets tcltk utils methods base other attached packages: [1] arrayQuality_1.14.0 RColorBrewer_1.0-2 gridBase_0.4-3 hexbin_1.12.0 lattice_0.17-4 convert_1.14.0 Biobase_1.16.3 [8] marray_1.16.0 limma_2.12.0 svSocket_0.9-5 svIO_0.9-5 R2HTML_1.58 svMisc_0.9-5 svIDE_0.9-5 > targetInfo <- read.marrayInfo ("targets2.txt") > mraw <- read.GenePix (targets=targetInfo) Reading ... B1a.gpr Reading ... B1b.gpr Reading ... B1cDS.gpr Reading ... B2a.gpr Reading ... B2b.gpr Error in Gf[, f] <- as.matrix(dat[, name.Gf]) : number of items to replace is not a multiple of replacement length What's that error actually saying, and how to correct it ! Christina [[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

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