beadarray: combining swaths for gene expression
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@thomas-kelder-5506
Last seen 9.6 years ago
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
beadarray beadarray • 785 views
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