FAQ

[BioC] question with reading bead summary data into beadarray

Ou, Jianhong
May 1, 2012 at 4:36 pm
Hi Mark,

I am dealing with Illumina BeadArray data by beadarray package. I download the training data (AsuragenMAQC_BeadStudioOutput.zip) from http://www.switchtoi.com/datasets.ilmn and followed the your sample code:
library("beadarray")
Loading required package: Biobase
Loading required package: BiocGenerics

Attaching package: �BiocGenerics�

The following object(s) are masked from �package:stats�:

xtabs

The following object(s) are masked from �package:base�:

anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find, get, intersect, lapply, Map, mapply, mget, order, paste,
pmax, pmax.int, pmin, pmin.int, Position, rbind, Reduce, rep.int, rownames, sapply, setdiff, table, tapply, union, unique

Welcome to Bioconductor

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

Loading required package: ggplot2
Welcome to beadarray version 2.6.0
beadarray versions >= 2.0.0 are substantial updates from beadarray 1.16.0 and earlier. Please see package vignette for details
setwd("~/Downloads/AsuragenMAQC_BeadStudioOutput")
dataFile = "AsuragenMAQC-probe-raw.txt"
qcFile = "AsuragenMAQC-controls.txt"
BSData = readBeadSummaryData(dataFile,qcFile, controlID="ProbeID",skip=0,qc.skip=0,qc.columns=list(exprs="AVG_Signal",Dectection="Detection Pval"))
Error in QC[[index]] = data[[i]] :
attempt to select less than one element
In addition: Warning message:
In readQC(file = qcFile, sep = qc.sep, skip = qc.skip, columns = qc.columns, :
controlIDs non-unique: 6 repeated entries have been removed.

and
sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: i386-apple-darwin9.8.0/i386 (32-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] beadarray_2.6.0 ggplot2_0.9.0 Biobase_2.16.0 BiocGenerics_0.2.0

loaded via a namespace (and not attached):
[1] AnnotationDbi_1.18.0 BeadDataPackR_1.8.0 colorspace_1.1-1 DBI_0.2-5 dichromat_1.2-4 digest_0.5.2
[7] grid_2.15.0 IRanges_1.14.2 limma_3.12.0 MASS_7.3-18 memoise_0.1 munsell_0.3
[13] plyr_1.7.1 proto_0.3-9.2 RColorBrewer_1.0-5 reshape2_1.2.1 RSQLite_0.11.1 scales_0.2.0
[19] stats4_2.15.0 stringr_0.6

Could you help me to figure out this problem? Thanks.

Yours sincerely,

Jianhong Ou

jia...@...edu
reply

Search Discussions

2 responses

  • Mark Dunning at May 3, 2012 at 10:33 am
    Hi,

    It looks like there is a typo in your command. The qc.columns argument
    should be;

    qc.columns=list(exprs="AVG_Signal",Detection="Detection Pval")

    and you had mis-typed Dectection as Dectection. Sorry the error
    message wasn't more informative in diagnosing the problem. The names
    of the qc columns have to match the names in the ExpressionSet object
    so that the control probes can get appended correctly to the main
    expression matrix.

    Regards,

    Mark

    On Tue, May 1, 2012 at 5:36 PM, Ou, Jianhong wrote:
    Hi Mark,

    I am dealing with Illumina BeadArray data by beadarray package. I download the training data (AsuragenMAQC_BeadStudioOutput.zip) from http://www.switchtoi.com/datasets.ilmn and followed the your sample code:
    library("beadarray")
    Loading required package: Biobase
    Loading required package: BiocGenerics

    Attaching package: ?BiocGenerics?

    The following object(s) are masked from ?package:stats?:

    ? ?xtabs

    The following object(s) are masked from ?package:base?:

    ? ?anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find, get, intersect, lapply, Map, mapply, mget, order, paste,
    ? ?pmax, pmax.int, pmin, pmin.int, Position, rbind, Reduce, rep.int, rownames, sapply, setdiff, table, tapply, union, unique

    Welcome to Bioconductor

    ? ?Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")',
    ? ?and for packages 'citation("pkgname")'.

    Loading required package: ggplot2
    Welcome to beadarray version 2.6.0
    beadarray versions >= 2.0.0 are substantial updates from beadarray 1.16.0 and earlier. Please see package vignette for details
    setwd("~/Downloads/AsuragenMAQC_BeadStudioOutput")
    dataFile = "AsuragenMAQC-probe-raw.txt"
    qcFile = "AsuragenMAQC-controls.txt"
    BSData = readBeadSummaryData(dataFile,qcFile, controlID="ProbeID",skip=0,qc.skip=0,qc.columns=list(exprs="AVG_Signal",Dectection="Detection Pval"))
    Error in QC[[index]] = data[[i]] :
    ?attempt to select less than one element
    In addition: Warning message:
    In readQC(file = qcFile, sep = qc.sep, skip = qc.skip, columns = qc.columns, ?:
    ?controlIDs non-unique: 6 repeated entries have been removed.

    and
    sessionInfo()
    R version 2.15.0 (2012-03-30)
    Platform: i386-apple-darwin9.8.0/i386 (32-bit)

    locale:
    [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

    attached base packages:
    [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base

    other attached packages:
    [1] beadarray_2.6.0 ? ?ggplot2_0.9.0 ? ? ?Biobase_2.16.0 ? ? BiocGenerics_0.2.0

    loaded via a namespace (and not attached):
    ?[1] AnnotationDbi_1.18.0 BeadDataPackR_1.8.0 ?colorspace_1.1-1 ? ? DBI_0.2-5 ? ? ? ? ? ?dichromat_1.2-4 ? ? ?digest_0.5.2
    ?[7] grid_2.15.0 ? ? ? ? ?IRanges_1.14.2 ? ? ? limma_3.12.0 ? ? ? ? MASS_7.3-18 ? ? ? ? ?memoise_0.1 ? ? ? ? ?munsell_0.3
    [13] plyr_1.7.1 ? ? ? ? ? proto_0.3-9.2 ? ? ? ?RColorBrewer_1.0-5 ? reshape2_1.2.1 ? ? ? RSQLite_0.11.1 ? ? ? scales_0.2.0
    [19] stats4_2.15.0 ? ? ? ?stringr_0.6

    Could you help me to figure out this problem? Thanks.

    Yours sincerely,

    Jianhong Ou

    jianhong.ou at umassmed.edu<mai...@...edu>



    ? ? ? ?[[alternative HTML version deleted]]


    _______________________________________________
    Bioconductor mailing list
    Bioconductor at r-project.org
    https://stat.ethz.ch/mailman/listinfo/bioconductor
    Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
  • Ou, Jianhong at May 3, 2012 at 12:50 pm
    Hi Mark,

    Thanks a lot. I got it.

    Yours sincerely,

    Jianhong Ou

    jianhong.ou at umassmed.edu

    On May 3, 2012, at 6:33 AM, Mark Dunning wrote:

    Hi,

    It looks like there is a typo in your command. The qc.columns argument
    should be;

    qc.columns=list(exprs="AVG_Signal",Detection="Detection Pval")

    and you had mis-typed Dectection as Dectection. Sorry the error
    message wasn't more informative in diagnosing the problem. The names
    of the qc columns have to match the names in the ExpressionSet object
    so that the control probes can get appended correctly to the main
    expression matrix.

    Regards,

    Mark

    On Tue, May 1, 2012 at 5:36 PM, Ou, Jianhong wrote:
    Hi Mark,

    I am dealing with Illumina BeadArray data by beadarray package. I download the training data (AsuragenMAQC_BeadStudioOutput.zip) from http://www.switchtoi.com/datasets.ilmn and followed the your sample code:
    library("beadarray")
    Loading required package: Biobase
    Loading required package: BiocGenerics

    Attaching package: ?BiocGenerics?

    The following object(s) are masked from ?package:stats?:

    xtabs

    The following object(s) are masked from ?package:base?:

    anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find, get, intersect, lapply, Map, mapply, mget, order, paste,
    pmax, pmax.int, pmin, pmin.int, Position, rbind, Reduce, rep.int, rownames, sapply, setdiff, table, tapply, union, unique

    Welcome to Bioconductor

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

    Loading required package: ggplot2
    Welcome to beadarray version 2.6.0
    beadarray versions >= 2.0.0 are substantial updates from beadarray 1.16.0 and earlier. Please see package vignette for details
    setwd("~/Downloads/AsuragenMAQC_BeadStudioOutput")
    dataFile = "AsuragenMAQC-probe-raw.txt"
    qcFile = "AsuragenMAQC-controls.txt"
    BSData = readBeadSummaryData(dataFile,qcFile, controlID="ProbeID",skip=0,qc.skip=0,qc.columns=list(exprs="AVG_Signal",Dectection="Detection Pval"))
    Error in QC[[index]] = data[[i]] :
    attempt to select less than one element
    In addition: Warning message:
    In readQC(file = qcFile, sep = qc.sep, skip = qc.skip, columns = qc.columns, :
    controlIDs non-unique: 6 repeated entries have been removed.

    and
    sessionInfo()
    R version 2.15.0 (2012-03-30)
    Platform: i386-apple-darwin9.8.0/i386 (32-bit)

    locale:
    [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

    attached base packages:
    [1] stats graphics grDevices utils datasets methods base

    other attached packages:
    [1] beadarray_2.6.0 ggplot2_0.9.0 Biobase_2.16.0 BiocGenerics_0.2.0

    loaded via a namespace (and not attached):
    [1] AnnotationDbi_1.18.0 BeadDataPackR_1.8.0 colorspace_1.1-1 DBI_0.2-5 dichromat_1.2-4 digest_0.5.2
    [7] grid_2.15.0 IRanges_1.14.2 limma_3.12.0 MASS_7.3-18 memoise_0.1 munsell_0.3
    [13] plyr_1.7.1 proto_0.3-9.2 RColorBrewer_1.0-5 reshape2_1.2.1 RSQLite_0.11.1 scales_0.2.0
    [19] stats4_2.15.0 stringr_0.6

    Could you help me to figure out this problem? Thanks.

    Yours sincerely,

    Jianhong Ou

    jianhong.ou at umassmed.edu<mai...@...edu>



    [[alternative HTML version deleted]]


    _______________________________________________
    Bioconductor mailing list
    Bioconductor at r-project.org
    https://stat.ethz.ch/mailman/listinfo/bioconductor
    Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

Related Discussions

Discussion Navigation
viewthread | post

2 users in discussion

Ou, Jianhong: 2 posts Mark Dunning: 1 post