Need help in preprocessing Illumina HumanHT-12 V4.0 expression beadchip

Question

[BioMed]

Dear all,

So far, I've been working with Affymetrix-based microarray. Nevertheless, my new project requires processing the data generated from Illumina HumanHT-12 V4.0 expression beadchip. Please let me know or give me some tips about what should I do to get a ready-to-use spreadsheet file from the raw data (eg., GSE65517, gathered from GEO) for further data processing and analysis.

I took a look at the user's guide of limma and google but it's not very helpful for me.

Thank you.

Answer 1

[AHW]

You may use lumi R package http://bioconductor.org/packages/release/bioc/html/lumi.html to process Illumina raw data. For example

 ## reads input file
 file.lumi <- lumiR(file)


 ##Generate expression values
 lumiExpr <- lumiExpresso(file.lumi, bg.correct = TRUE, 
                                 normalize = TRUE, verbose = TRUE)    
 exprs <- exprs(lumiExpr)

## generate p-values
pvalue <- detection(lumiExpr)

For more details check lumi R package given above.

[BioMed]

Thank you very much. I will try to use lumi.