Post the header of the unsuccesful gpr file -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch on behalf of alison waller Sent: Fri 30/11/2007 9:13 PM To: bioconductor at stat.math.ethz.ch Subject: [BioC] Limma - error reading in .gpr files Hi all, I'm having a problem reading in my genepix files using read.maimages. If anyone could help interpret my error message that would be great thanks, Are these numbers specifiying a location in the spreadsheet where there might be a problem. Thanks so much, alison > library(limma) > targets<-readTargets("VCMeOHTargets.txt") > RG<-read.maimages(targets$FileName) Error in read.maimages(targets$FileName) : must specify columns for generic input > RG<-read.maimages(targets$FileName,source="genepix") Read 830scan3.gpr Read 778scan2.gpr Read 784scan2.gpr Error in "[<-"(`*tmp*`, , i, value = c(106, 11029, 33, 33, 131, 87, 306, : number of items to replace is not a multiple of replacement length > ****************************************** Alison S. Waller M.A.Sc. Doctoral Candidate awaller at chem-eng.utoronto.ca 416-978-4222 (lab) Department of Chemical Engineering Wallberg Building 200 College st. Toronto, ON M5S 3E5 [[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

Hi all, I'm having getting confused with the imagebplot3by2 command. I am able to use imageplot to plot (R,G, Rb, log2R etc.) for the individual arrays, but I cannot use imageplot3by2. I'm not sure if I am using the incorrect syntax or if there is an error in my data that is making this function impossible. I've pasted all my attempts below. If anyone can help interpret the error messages that would be great. I think that the na.rm=TRUE is telling me something about missing values, and I'm not too sure about c(0.05,0.95). This is some vector c, and specific values? Thanks, Alison > library(limma) > targets<-readTargets("VCMeOHTargets.txt") > RG<-read.maimages(targets$FileName,source='genepix') Read 830scan3.gpr Read 778scan2.gpr Read 784scan2.gpr Read 729Sscan2.gpr Read 797scan2bckp.gpr Read 791scan2bckp.gpr > plot (log2(RG$G[,1]),log2(RG$R[,1])) > imageplot3by2(log2(RG$R),low='white',hig='red') Error in RG[[z]] : subscript out of bounds > RG.b<-backgroundCorrect(RG,method='minimum') > dim(RG$R) [1] 19200 6 > imageplot(log2(RG$R[,1]),RG$printer,low='white',high='red') > RG An object of class "RGList" $R 830scan3 778scan2 784scan2 729Sscan2 797scan2bckp 791scan2bckp [1,] 94 73 88 122 113 106 [2,] 10133 12009 17661 17656 7191 11029 [3,] 31 30 45 53 67 33 [4,] 45 34 44 54 60 33 [5,] 177 107 134 209 86 131 19195 more rows ... $G 830scan3 778scan2 784scan2 729Sscan2 797scan2bckp 791scan2bckp [1,] 96 87 106 101 125 100 [2,] 8720 9383 8453 13508 5462 6119 [3,] 33 34 46 49 89 36 [4,] 51 37 44 48 90 38 [5,] 124 86 99 143 122 98 19195 more rows ... $Rb 830scan3 778scan2 784scan2 729Sscan2 797scan2bckp 791scan2bckp [1,] 27 25 54 53 63 32 [2,] 26 26 40 54 63 32 [3,] 25 24 36 47 64 28 [4,] 25 24 37 47 61 26 [5,] 25 25 41 53 52 26 19195 more rows ... $Gb 830scan3 778scan2 784scan2 729Sscan2 797scan2bckp 791scan2bckp [1,] 27 26 88 38 92 35 [2,] 29 28 48 39 94 33 [3,] 26 27 41 37 92 30 [4,] 26 28 40 41 83 29 [5,] 25 27 51 49 69 29 19195 more rows ... $targets FileName 830scan3 830scan3.gpr 778scan2 778scan2.gpr 784scan2 784scan2.gpr 729Sscan2 729Sscan2.gpr 797scan2bckp 797scan2bckp.gpr 791scan2bckp 791scan2bckp.gpr $genes Block Row Column ID Name 1 1 1 1 03H13 Kbgs-005-H13 2 1 1 2 03H01 Kbgs-005-H1 3 1 1 3 03D13 Kbgs-005-D13 4 1 1 4 03D01 Kbgs-005-D1 5 1 1 5 02P13 Kbgs-004-P13 19195 more rows ... $source [1] "genepix" $printer $ngrid.r [1] 12 $ngrid.c [1] 4 $nspot.r [1] 20 $nspot.c [1] 20 $ndups [1] 1 $spacing [1] 1 attr(,"class") [1] "PrintLayout" > imageplot3by2(RG,RG$R,low='white',high='red',common.lim=TRUE) Error in quantile(RG[[z]], c(0.05, 0.95), na.rm = TRUE) : no such index at level 1 > z<-RG > imageplot3by2(RG,z=RG$R,zlim=NULL,common.lim=TRUE) Error in quantile(RG[[z]], c(0.05, 0.95), na.rm = TRUE) : no such index at level 1