[BioC] beadarray package

[RS [guest]]

Hi Mark and Matt,

I have four samples with three replicates for which Illumina beadarray expression data was collected. The array design corresponds to the HumanHT12 chip with Humanv4 annotation.

I started with beadlevel data with .tif files, .locs files and _perBeadFile.txt and was able to use processSwathData() function to obtain 24 _Swath.tif files. My sampleSheet.csv had issues although I prepared it based on the beadlevel example data you provide. So, I didn't provide this file and used readIllumina() to read the 24 _Swath.tif files. It read the files fine but it's not clear how to combine the two files into one intensity file per array/sample? I would like to create an expressionSet and perform differential expression using limma.

I would appreciate any help.

Thanks,
Raj


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