[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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