Hello all,

I am running an analysis of some cell assay experiments. I am getting an 
error in configuring the cellHTS object. I am attaching the Rt trancript 
file of the session as well as my description and plate configuration 
files. Any help will be greatly appreciated.
Thanks,

Shripad Sinari
--------------------------------------------------------------------------------
R version 2.6.0 (2007-10-03)
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 > if(!exists("baseenv", mode="function")) baseenv <- function() NULL
 > options(STERM='iESS', editor='emacsclient')
 > library(cellHTS2)
Loading required package: prada
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: RColorBrewer
Loading required package: grid
Loading required package: rrcov
Loading required package: robustbase
Scalable Robust Estimators with High Breakdown Point (version 0.4-01)
KernSmooth 2.22 installed
Copyright M. P. Wand 1997
Loading required package: genefilter
Loading required package: survival
Loading required package: splines

Attaching package: 'survival'


        The following object(s) are masked from package:robustbase :

         heart

Loading required package: splots
Loading required package: vsn
Loading required package: affy
Loading required package: affyio
Loading required package: preprocessCore
Loading required package: limma
 >
 >
 > importData <- function(fname){
+ d <- count.fields(fname, sep = ",", quote = "",
+                   skip = 0, blank.lines.skip = TRUE,
+                   comment.char = "")
+ nCol <- max(d)
+ pp <- min(which(d==nCol))
+
+ x <- scan(fname, what = as.list(rep("", nCol)), skip = pp-1,
+   sep=",", quote="", fill = TRUE, strip.white = TRUE, quiet=TRUE)
+
+ #info = matrix(t(unlist(x)), nrow=length(x), byrow=TRUE)
+
+ # Matrix reproducing the plate
+ x <- sapply(x, function(y) as.numeric(y))
+
+ nums <- rep(1:ncol(x), nrow(x))
+ nums <- sapply(nums, function(i) if(i<10) paste(0, i, sep="") else i)
+ lets <- rep(LETTERS[1:nrow(x)], each=ncol(x))
+ wells <- paste(lets, nums, sep="")
+ # put as a row-wise vector
+ x <- as.vector(t(x))
+ out <- data.frame(well=I(wells), val=as.numeric(x))
+ info <- cbind(basename(fname), out)
+ tfile <- tempfile(pattern = "file", tmpdir = tempdir())
+ write.table(info, tfile, col.names=FALSE, row.names=FALSE, sep="\t", 
quote=FALSE)
+ info <- readLines(tfile)
+ unlink(tfile)
+ out <- list(out, info)
+ return(out)
+ }
 >
 > x <- 
readPlateList("Platelist.txt",path=".",name="Drug",importFun=importData)
Found data in 8 x 12 (96 well) format.
 Reading file 1: PlateCtlKcP1A.csv; Reading file 2: PlateCtlKcP1B.csv; 
Reading file 3: PlateCtlKcP1C.csv; Reading file 4: PlateCtlKcP2A.csv; 
Reading file 5: PlateCtlKcP2B.csv; Reading file 6: PlateCtlKcP2C.csv; 
Reading file 7: PlateCtlKcS1A.csv; Reading file 8: PlateCtlKcS1B.csv; 
Reading file 9: PlateCtlKcS1C.csv; Reading file 10: PlateCtlKcS2A.csv; 
Reading file 11: PlateCtlKcS2B.csv; Reading file 12: PlateCtlKcS2C.csv; 
Reading file 13: PlateCtlKcS3A.csv; Reading file 14: PlateCtlKcS3B.csv; 
Reading file 15: PlateCtlKcS3C.csv; Reading file 16: PlateCtlS2P1A.csv; 
Reading file 17: PlateCtlS2P1B.csv; Reading file 18: PlateCtlS2P1C.csv; 
Reading file 19: PlateCtlS2P2A.csv; Reading file 20: PlateCtlS2P2B.csv; 
Reading file 21: PlateCtlS2P2C.csv; Reading file 22: PlateCtlS2S1A.csv; 
Reading file 23: PlateCtlS2S1B.csv; Reading file 24: PlateCtlS2S1C.csv; 
Reading file 25: PlateCtlS2S2A.csv; Reading file 26: PlateCtlS2S2B.csv; 
Reading file 27: PlateCtlS2S2C.csv; Reading file 28: PlateCtlS2S3A.csv; 
Reading file 29: PlateCtlS2S3B.csv; Reading file 30: PlateCtlS2S3C.csv; 
Reading file 31: PlateHPK56KcP1A.csv; Reading file 32: 
PlateHPK56KcP1B.csv; Reading file 33: PlateHPK56KcP1C.csv; Reading file 
34: PlateHPK56KcP2A.csv; Reading file 35: PlateHPK56KcP2B.csv; Reading 
file 36: PlateHPK56KcP2C.csv; Reading file 37: PlateHPK56KcS1A.csv; 
Reading file 38: PlateHPK56KcS1B.csv; Reading file 39: 
PlateHPK56KcS1C.csv; Reading file 40: PlateHPK56KcS2A.csv; Reading file 
41: PlateHPK56KcS2B.csv; Reading file 42: PlateHPK56KcS2C.csv; Reading 
file 43: PlateHPK56KcS3A.csv; Reading file 44: PlateHPK56KcS3B.csv; 
Reading file 45: PlateHPK56KcS3C.csv; Reading file 46: 
PlateHPK56S2P1A.csv; Reading file 47: PlateHPK56S2P1B.csv; Reading file 
48: PlateHPK56S2P1C.csv; Reading file 49: PlateHPK56S2P2A.csv; Reading 
file 50: PlateHPK56S2P2B.csv; Reading file 51: PlateHPK56S2P2C.csv; 
Reading file 52: PlateHPK56S2S1A.csv; Reading file 53: 
PlateHPK56S2S1B.csv; Reading file 54: PlateHPK56S2S1C.csv; Reading file 
55: PlateHPK56S2S2A.csv; Reading file 56: PlateHPK56S2S2B.csv; Reading 
file 57: PlateHPK56S2S2C.csv; Reading file 58: PlateHPK56S2S3A.csv; 
Reading file 59: PlateHPK56S2S3B.csv; Reading file 60: PlateHPK56S2S3C.csv;
Done.

 >
 > x <- configure(x,descripFile="Description.txt",confFile="Plateconf.txt")
Error in read.table(file.path(ppath, confFile), sep = "\t", header = 
TRUE,  :
  duplicate 'row.names' are not allowed
 > sessionInfo()
R version 2.6.0 (2007-10-03)
x86_64-redhat-linux-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

attached base packages:
 [1] splines   grid      tools     stats     graphics  grDevices utils   
 [8] datasets  methods   base    

other attached packages:
 [1] cellHTS2_2.2.1       vsn_3.2.1            limma_2.12.0       
 [4] affy_1.16.0          preprocessCore_1.0.0 affyio_1.6.1       
 [7] splots_1.4.0         genefilter_1.16.0    survival_2.32      
[10] prada_1.14.0         rrcov_0.4-01         robustbase_0.2-8   
[13] RColorBrewer_1.0-2   Biobase_1.16.1     

loaded via a namespace (and not attached):
[1] annotate_1.16.1     AnnotationDbi_1.0.6 DBI_0.2-4         
[4] geneplotter_1.16.0  KernSmooth_2.22-21  lattice_0.16-5    
[7] MASS_7.2-36         RSQLite_0.6-4       stats4_2.6.0      
 > q()
Save workspace image? [y/n/c]: n

Process R finished at Thu Jan  3 11:54:29 2008
-----------------------------------------------------
Description file:

[Lab description]
Experimenter name: Tom Bunch
Laboratory: Functional Genomics Shared Service
Contact information: Arizona Cancer Center

[Screen description]
Screen: DualChanData
Title: Example data set for a dual-color screen
Version: 0
Date: Dec 2007
Screentype: RNA interference
Organism: Drosophila melanogaster
Celltype: Kc
Library: HFA
Assay: Reporter 1 for RNAi and Reporter 2 for drug activity
Assaytype: homogenous
Assaydescription:  Cells were treated with dsRNAs in three 96-well plates

[Publication description]
Publicationtitle:
Reference:
PMIDs:
URL:
License: GPL
Abstract:

[Files]
plateList: Platelist.txt
plateConf: Plateconf.txt
----------------------------------------------------------------
Plate configuration file:
Wells: 96
Plates: 10
Plate   Well    Content
*       *       sample
*       G0[1-9] pos
*       G1[0-2] pos
*       H01     noCells+DM
*       H02     noCells+DM
*       H0[3-9] noCells+GM
*       H1[0-2] noCells+GM

-----------------------------------------------------------



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