Question: Inquiry about lumiT function
5.8 years ago by
Guest User • 12k
Guest User • 12k wrote:
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) locale:  LC_COLLATE=Romanian_Romania.1250 LC_CTYPE=Romanian_Romania.1250  LC_MONETARY=Romanian_Romania.1250 LC_NUMERIC=C  LC_TIME=Romanian_Romania.1250 attached base packages:  stats graphics grDevices utils datasets methods base -- Sent via the guest posting facility at bioconductor.org.
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