[BioC] Beadarray expression data

Ina Hoeschele inah at vt.edu
Tue Aug 7 22:14:04 CEST 2007


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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