[BioC] Illumina bead arrays

[Pan Du]

Hi Ina,

You can try the lumiR function in the lumi package, which can automatically
detect the BeadStudio versions.
For example:
X.lumi = lumiR(fileName)

The latest version of lumi can be downloaded from:
    http://www.bioconductor.org/packages/2.1/bioc/html/lumi.html


Pan



On 8/14/07 5:00 AM, "bioconductor-request at stat.math.ethz.ch"
<bioconductor-request at stat.math.ethz.ch> wrote:

> Message: 5
> Date: Mon, 13 Aug 2007 10:46:24 -0400
> From: Ina Hoeschele <inah at vt.edu>
> Subject: [BioC] Illumina bead arrays
> To: bioconductor at stat.math.ethz.ch
> Message-ID: <46C06EC0.6020109 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 
> Hi,
>    I am still struggling with my first try at working with Illumina bead
> array expression data, specifically getting the data read by the R
> package beadarray.
> 
> The data was created by an off-site collaborator using BeadStudio
> version  3.0.14. My collaborator sent two types of files to me:
> (1) a number of .csv files (read by excel, 2 for each sample) with
> columns Illumicode, N, mean GRN, Dev GRN.
> (2) a summary .txt file with columns TargetID
> MIN_Signal-1814647013_A    AVG_Signal-1814647013_A
> MAX_Signal-1814647013_A    NARRAYS-1814647013_A
> ARRAY_STDEV-1814647013_A    BEAD_STDEV-1814647013_A
> Avg_NBEADS-1814647013_A    Detection-1814647013_A, with the
> MIN_Signal-... to Detection-... columns repeated for the remaining samples.
> 
> I read the summary data(2) with the statement
> readBeadSummaryData(dataFile, skip=8, columns = list(exprs =
> "AVG_Signal", BeadStDev = "BEAD_STDEV", NoBeads = "Avg_NBEADS"), sep="\t"),
> but every time I do this R gets hung up (no error message).
> 
> I also tried reading the bead-level data (the .csv files) with the statement
> BLData <- readIllumina(textType = ".csv")
> but then I get the error message
> Error in strtrim(x, width) : invalid 'width' argument
> 
> Any suggestions would be much appreciated.
> Thank you.
> Ina
>