Help with processing GSE63060: Illumina data that does not have lumi requirements

Question

[mincej20]

Hello, I'm new to microarray analysis in R, and I'm trying to process the raw data found in GSE63060 (AddNeuroMed cohort). These are on Illumina HumanHT-12 v3.0 Gene Expression BeadChip. However, most of the processes that I see relating to background correction and normalization for these arrays, like lumi, requires either the output files from BeadStudio or a matrix of expression values with Detection.Pvals columns. The raw data provided on NCBI GEO for this project is a data matrix with an IND_ID column and subsequent columns for the AVG_Signal expression values for each subject, as well as a BGX annotation file, so this data doesn't conform to the lumi requirements listed above. How do I go about the background correction and normalization with this format?

Thank you for any help!

Answer 1

[Kevin Blighe]

As you are new to microarray analysis, I would encourage you to retrieve the data automatically via the GEO2R program - see the big blue button on the main accession page.

After that, click on the R script tab, where you will find code to retrieve the [assumed] normalised data.

Once you have retrieved the normalised data, please use limma to perform differential expression analysis.

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I have posted previous answers on this topic, here:

• Illumina HumanHT-12 V4.0 expression beadchip
• illumina Arrays Illumina HumanHT-12 V3.0 expression beadchip reading data

Kevin