Question: Inquiry about lumiT function

0

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:
[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.

ADD COMMENT
• link
•
modified 5.3 years ago
by
Pan Du •

**440**• written 5.3 years ago by Guest User •**12k**