[BioC] Illumina bead arrays

[Matt Ritchie]

Hi Ina,

Sorry to hear you are having such a struggle reading in your Illumina data.
I noticed a problem reading in BeadStudio 3 output a few weeks ago and
checked in a fix to the developmental version of beadarray.

So if you upgrade to the latest version of beadarray (1.5.8, available from
http://bioconductor.org/packages/2.1/bioc/html/beadarray.html) your summary
data should read in without incident.  Note that the default arguments to
readBeadSummaryData() have been set for BeadStudio 3 output, so all you need
to set it the filename.

I have also added some more meaningful warnings to readIllumina(), which
will help diagnose the cause of the second error you mention (most likely
you are missing the tiff files, so try useImages=FALSE).

Best wishes,

Matt

> 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