[BioC] beadarray: combining swaths for gene expression

Thomas Kelder thomaskelder at gmail.com
Wed Sep 19 09:54:16 CEST 2012

Dear members,

I'm trying to use the beadarray package to preprocess the raw data
from Illumina Mousev2 gene expression arrays. Apparently these arrays
are scanned with the iScan system, so I first ran the function
processSwathData before using readIllumina to obtain the bead level
data and summary to obtain the bead summary data. The resulting
expression matrix and accompanying data (se.exprs, detection scores)
now contain two columns per array slot (e.g. "8491191051_A-Swath1" and
"8491191051_A-Swath2"). After reading the documentation, I understand
that this is because the array is scanned in two partly overlapping
parts, however, I could not find information on how to combine these
into one expression matrix per slot. Illumina's BeadStudio software
seems to do this automatically, but provides no information how.
Should I simply take the average of the Swath1 and Swath2, or is there
perhaps an argument to one of the beadarray functions that will
combine them? Thanks in advance for your help!

Best wishes,
Thomas Kelder

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