[BioC] Help needed with configuration function from cellHTS2 package

ligia at ebi.ac.uk ligia at ebi.ac.uk
Thu Jan 3 21:38:48 CET 2008


Hi Shripad,

The problem is in your Plateconf.txt file: it has one extra (empty) column
at the end of line 5.
If you remove it (or use the attached file), it should work properly!

Cheers,
Ligia


> 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)
> Copyright (C) 2007 The R Foundation for Statistical Computing
> ISBN 3-900051-07-0
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> Type 'q()' to quit R.
>
>  > 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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>
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