[BioC] Illumina bead arrays

[Johnstone, Alice]

Just wondering, does your data file contain 8 rows of header space?  The
standard seems to be 7 with the AVG_ headers in row 8 (you can check by
opening in excel) so skip=7.
If you want to look at the bead level data you require the TIFF files
and the csv files.  This is not the standard format given as it requires
adjustments to the machine and hence has to be requested before the
chips are read. It may be that they have only given you summary data,
and hence why there are errors with trying to read at bead-level.
Im in the processes of annalysing my own Illumina data, (which I agree,
is difficult with not as much info out there yet) hope I can help!
Regards
Alice

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Pan Du
Sent: Wednesday, 15 August 2007 2:35 a.m.
To: bioconductor at stat.math.ethz.ch
Cc: Ina Hoeschele
Subject: Re: [BioC] Illumina bead arrays

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
>

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