[BioC] Beadarray expression data

[Mark Dunning]

Hi,

The beadarray package can read the output from BeadStudio version 3.  
In fact all you need to do is change the skip parameter so that it  
ignores the first 8 lines of output from BeadStudio 3 , which are all  
header information

The following function call should do the trick.

B = readBeadSummaryData(dataFile, skip=8, sep="\t")

When specifying the column names to read, you just need to specify  
the expression values are found in columns with the prefix  
"AVG_Signal". The function then searches through the column names and  
finds all instances of this string and creates an matrix with the  
appropriate number of columns.

Hope this helps,

Mark


On 7 Aug 2007, at 21:14, Ina Hoeschele wrote:

> Hi all,
>    I am completely new to the analysis of Illumina Beadarray gene
> expression data (but quite familiar with Affy data).  Such data (with
> samples run on 3 chips)  was sent to me by a collaborator. From the
> vignettes for Bioconductor packages 'beadarray' and 'BeadExplorer', it
> looks like these accommodate  Beadstudio version 1 and 2 data,  
> while our
> data was created by BeadStudio version  3.0.14.. Would it still  
> work? 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.
> It looks like beadarray expects to read the summary data from a .csv
> rather than a .txt file? From the example given on page 2 of the
> beadarray vignette, the summary data are read in by
> BSData <- readBeadSummaryData(datafile, ..., columns = list(exprs =
> AVG_Signal", BeadStDev = "BEAD_STDEV", NoBeads = "Avg_NBEADS", ...)
>
> Since I have AVG_Signal-1814647013_A, AVG_Signal-1814647013_B etc. and
> not just one AVG_Signal, how do I specify the columns to be read?
>
> Sorry for these ignorant questions, but this is my first try at these
> data. Thanks for any advice!
> Ina
>
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