Hi, I am trying to run limma under R following the User guide. Everything Ok until I get the message at the end, and I can figure out wich one is the error. Could anyone help me? Thanks Veronica > library (limma) > dir() [1] "Data GPR" "ExpDescFile.xls" [3] "M1.4 VI2.4 (5-10-07) VI" "M1.8 VI1.8 (5-25-07) VI" [5] "M2.4 VI1.4 (5-10-07) VI" "M2.8 VI2.8 (5-25-07) VI" [7] "M3.4 VI3.4 (5-10-07) VI" "M3.8 VI3.8 (5-25-07) VI" [9] "Microarray data -Project M vs V 2" "Microarray data -Project M vs VI" [11] "Microarray data -Project M vs VI 2" "nonM14VI14.gpr" [13] "nonM14VI14.txt" "nonM18VI18.gpr" [15] "nonM24VI24.gpr" "nonM28VI28.gpr" [17] "nonM34VI34.gpr" "nonM38VI38.gpr" [19] "PoSaVsample.txt" "PoSaVsampleII.txt" [21] "Test.xls" "Verification" > targets <- readTargets("PoSaVsample.txt") > ls() [1] "targets" > targets Slide.Number Name File.Name Cy3 Cy5 1 1 MV14 nonM14VI14.gpr virus mock 2 2 MV24 nonM24VI24.gpr virus mock 3 3 MV34 nonM34VI34.gpr virus mock 4 4 MV18 nonM18VI18 virus mock 5 5 MV28 nonM28VI28 virus mock 6 6 MV38 nonM38VI38 virus mock > RG <-read.maimages(targets$File.Name, source="genepix") Error in RG[[a]][, i] <- obj[, columns[[a]]] : number of items to replace is not a multiple of replacement length > Veronica Costantini Graduate Research Associate Food Animal Health Research Program Dept of Veterinary Preventive Medicine The Ohio State University Wooster, Ohio, 44691 Phone: (330) 263-3744 Fax: (330) 263-3677

Quoting VERONICA COSTANTINI <costantini.3 at="" osu.edu="">: > Hi, I am trying to run limma under R following the User guide. > Everything Ok until I get the message at the end, and I can figure > out wich one is the error. Could anyone help me? > > Thanks > Veronica > > >> library (limma) >> dir() > [1] "Data GPR" "ExpDescFile.xls" > [3] "M1.4 VI2.4 (5-10-07) VI" "M1.8 VI1.8 (5-25-07) VI" > [5] "M2.4 VI1.4 (5-10-07) VI" "M2.8 VI2.8 (5-25-07) VI" > [7] "M3.4 VI3.4 (5-10-07) VI" "M3.8 VI3.8 (5-25-07) VI" > [9] "Microarray data -Project M vs V 2" "Microarray data -Project M vs VI" > [11] "Microarray data -Project M vs VI 2" "nonM14VI14.gpr" > [13] "nonM14VI14.txt" "nonM18VI18.gpr" > [15] "nonM24VI24.gpr" "nonM28VI28.gpr" > [17] "nonM34VI34.gpr" "nonM38VI38.gpr" > [19] "PoSaVsample.txt" "PoSaVsampleII.txt" > [21] "Test.xls" "Verification" >> targets <- readTargets("PoSaVsample.txt") >> ls() > [1] "targets" >> targets > Slide.Number Name File.Name Cy3 Cy5 > 1 1 MV14 nonM14VI14.gpr virus mock > 2 2 MV24 nonM24VI24.gpr virus mock > 3 3 MV34 nonM34VI34.gpr virus mock > 4 4 MV18 nonM18VI18 virus mock > 5 5 MV28 nonM28VI28 virus mock > 6 6 MV38 nonM38VI38 virus mock >> RG <-read.maimages(targets$File.Name, source="genepix") > Error in RG[[a]][, i] <- obj[, columns[[a]]] : > number of items to replace is not a multiple of replacement length Did you realise that your targets file specifies 3 non-existant files? nonM18VI18 nonM28VI28 nonM38VI38 don't forget to include the extension (".gpr" in this case). Jose -- Dr. Jose I. de las Heras Email: J.delasHeras at ed.ac.uk The Wellcome Trust Centre for Cell Biology Phone: +44 (0)131 6513374 Institute for Cell & Molecular Biology Fax: +44 (0)131 6507360 Swann Building, Mayfield Road University of Edinburgh Edinburgh EH9 3JR UK