Hi- 

 

I am new to analyzing Illumina microarray data.  We ran 6 case and 6 control samples (no replicates) on 1 Illumina HT-12 v3 Expression BeadChip.  I would like to analyze our data using lumi.  I was planning on doing the following: 1) background subtraction in Beadstudio, 2) VST in lumi, and 3) quantile normalization in lumi.  I noticed that the normalization methods in lumi are for between chip normalization.  Would it still be appropriate to use quantile normalization in my situation since I only have one chip (ie: between array normalization)?   

 

Also, will the VST method yield similar results if gene-level data are used instead of probe-level data?

 

Thanks for your time,

 

Christina Markunas

cam27@duke.edu



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