[BioC] Inquiry about lumiT function

Neagu Matei Stefan [guest] guest at bioconductor.org
Sat Jan 4 17:05:50 CET 2014

May I ask you a question about output of the function lumiT ?
I am using this function to do variance stabilization on some data from an Ilumina BeadStudio output file using the VST method. Because of the standard format of this file, I have 4 values for each probe, AVG_Signal, BEAD_STDERR,Avd_NBEADS and Detection_Pvalue which of course are the inputs for the lumiT function. Applying the VST method, the 3 parameters c1,c2 and c3 are calculated. Since the input file does not explicitily provide the bead-level values for each probe, but only their statistical characteristics, I do not understand exactly how the final value for each probe outputed by the lumiT function is calculated and if it represents the mean of the transformed bead-level values.
To be more precise I would like to ask if the final output is calculated with the formula:h=1/c1*arcsinh⁡(c2/√c3+(c1*m)/√c3), where m represents the mean of the beads values of the probe and h represents the output of lumiT for that probe.
Thank you very much for your kindness. 

 -- output of sessionInfo(): 

R version 3.0.2 (2013-09-25)
Platform: x86_64-w64-mingw32/x64 (64-bit)

[1] LC_COLLATE=Romanian_Romania.1250  LC_CTYPE=Romanian_Romania.1250   
[3] LC_MONETARY=Romanian_Romania.1250 LC_NUMERIC=C                     
[5] LC_TIME=Romanian_Romania.1250    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base  

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