[BioC] How to explain lumi expression values

[Gordon K Smyth]

Hi Varshna,

lumi doesn't help you decide what is expressed vs what is not. For that 
you need to make use of the Illumina negative control probes.

The simplest method is to use the Detection p-values for each expression 
value that are provided by the Illumina BeadStudio software and/or to use 
the propexpr() function in the limma package.  See Section 17.3.4 of the 
limma User's Guide for a case study of how to decide which Illumina probes 
are expressed.

Another consideration is that lumi compresses the range of the normalized 
intensity values considerably, so that the smallest log2 value become as 
large as 7.8 even for probes that are not expressed.  See Figure 1 of:

  http://nar.oxfordjournals.org/content/38/22/e204

for a careful discussion this.  This paper recommends the neqc() function 
as providing the same sort of precision as the lumi method but without so 
much compression.

Best wishes
Gordon

> Date: Fri, 2 May 2014 11:38:05 +0200
> From: Varshna Goelela <v.goelela at gmail.com>
> To: bioconductor at r-project.org
> Subject: [BioC] How to explain lumi expression values
>
> Hi All,
>
> I need some clarification for the sake of explaining to my PI (even though
> I read the documentation on the lumi/limma/beadarray packages I'm still
> not completely clear as to how to explain this).
>
> I have my Illumina expression data and the range of the log2
> transformed expression values fall between 7.81 to 15.8. He wants to know
> what is considered expressed and what is not expressed.
>
> Kind regards,
> Varshna

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