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

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!

lumi illumina bioconductor r
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updated by Kevin Blighe Kevin Blighe • written by mincej20 • mincej20

1 answer

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.

sss

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

sss

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

I have posted previous answers on this topic, here:

Kevin

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written by Kevin Blighe Kevin Blighe

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