Dear BioC users,

I am trying to find differentially expressed genes using data publicly available in NCBI GEO that comes from Illumina platforms. I would like to use the GEOquery package to download and import the data, the beadarray package to do the preprocessing and the limma package in order to find DE genes.

I am following the instructions given in the beadsummary vignette (beadsummary.pdf), but when I am trying to convert the ExpressionSet object (from getGEO function) to an ExpressionSetIllumina object (described in p.30-31)

>summaryData <- as(gse, "ExpressionSetIllumina") 

it throws the following error: 

Error in object@channelData[[1]] : subscript out of bounds

I cannot make it work, not even with the example provided by the vignette. Is there anyone who could help me?

Thank you in advance,

Anna

Thank you for the comment. You are right, but I think I finally found the answer here: beadarray error importing from GEOquery

The problem was fixed using the code that Mike Smith suggested.