Pan Du | 5 Jan 08:02 2014
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Re: Inquiry about lumiT function

Hi Neagu

You are correct: in 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.
For more details, please check the method paper:
http://nar.oxfordjournals.org/content/36/2/e11.long

Pan

On Sat, Jan 4, 2014 at 8:05 AM, Neagu Matei Stefan [guest] <
guest@...> 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:
> [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
>
> --
> Sent via the guest posting facility at bioconductor.org.
>

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