[BioC] Help needed with configuration function from cellHTS2 package
Shripad Sinari
shripad at email.arizona.edu
Fri Jan 4 01:09:09 CET 2008
Hello Dr.Huber,
Ms. Ligia's suggestion seemed to have solved the problem. My
Plateconf.txt had an extra column on line 5 and removing solves the
issue. However I am attaching and sending you the requested files. The
mailing list seems to filter out certain attachments. So if you do not
get all the files, please let me know.
Plateconf.txt.bak is the original plate configuration file.
Thank you,
Shripad Sinari
Wolfgang Huber wrote:
> Dear Shripad,
>
> thanks for the report! This is an odd error. Odd because the call to
> "read.table" in the configure method does not tell read.table to
> expect row.names.
>
> 1. Can you double-check that the file "Plateconf.txt" has exactly two
> header lines before the line with "Plate Well Content" (and not,
> for example, also some empty lines) and that the different columns,
> starting with line 3, are really separated by tabs (and not, e.g., by
> spaces)
>
> 2. If you like, please also send me the PlateCtlKcP1A.csv,
> PlateList.txt, Plateconf.txt, Description.txt files so that we can
> reproduce the error and perhaps make the code that reads them more
> forgiving of such variations, or at least produce a better error
> message (please attach them to the email rather than copy/pasting them
> into the email, since the latter may distort important formating
> details such as invisible tabulator characters).
>
> As an aside, there has been quite some development on cellHTS2 since
> the version 2.2.1 that you use (from the Bioc 2.1 release), so I would
> also suggest to get the newest version 2.3.16 from
> http://www.bioconductor.org/packages/2.2/bioc/html/cellHTS2.html
> (but I don't think this solves your problem),
>
> Best wishes
> Wolfgang.
>
>
>> 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
>>
>> R is free software and comes with ABSOLUTELY NO WARRANTY.
>> You are welcome to redistribute it under certain conditions.
>> Type 'license()' or 'licence()' for distribution details.
>>
>> Natural language support but running in an English locale
>>
>> R is a collaborative project with many contributors.
>> Type 'contributors()' for more information and
>> 'citation()' on how to cite R or R packages in publications.
>>
>> Type 'demo()' for some demos, 'help()' for on-line help, or
>> 'help.start()' for an HTML browser interface to help.
>> 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
>>
>> -----------------------------------------------------------
>>
>>
>>
>> [[alternative HTML version deleted]]
>>
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>
>
>
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