Hello,

 

I have been digging in Bayesreg.R for several days now, but cannot find
the solution for my problem. I want to calculate a Bayes PAIRED t-test
if this is possible (I have the impression that it is not). With a
paired t-test I am refering to a biological sample before and after
treatment from the same object. This test is performed for 4 different
objects, so in total I have 8 samples: 4 before treatment and 4 after
treatment. The samples are hybridized on a HG-U133 plus2 array and
quality control, GC-RMA normalization and IQR-filtering have been
applied. In total, 8912 genes remained for calculating the Bayes paired
p-values.

 

When looking at this site:
http://visitor.ics.uci.edu/genex/cybert/help/index.html I can find an
example on how a paired Bayes t-test can be performed (that is: if I
understand it correctly): add to the original non-2log transformed data
(so transform the GC-RMA values back to the non-log scale) an additional
'Expr Est' column (my statistical background is not as such that this
makes sense to me). Well, I did this (using numR=8 and doLog=TRUE) and
calculated p-values between 0 and roughly 10^-6... Of course, this can't
be true... Searching for additional help (which is hardly available for
paired t-tests) I found a CyberT refence saying that the paired t-test
refers to the 2-dye situation. It is paired because the same array is
used. Well, in my situation (Affymetrix) this is not true, but I can
calculate the ratio after / before treatment (on the same object) and
put it in. This did make sense, but now I find p-values between 0 and
1.5! It is weird that Bayesreg.R allows the generation of p-values
larger than 1, so I am wondering whether this is an artifact of Bayesian
statistics or that I am doing something wrong? Can someone please give
me a hint on how to do the paired Bayesian t-test properly (e.g. with a
small example dataset)?
 
Kind regards,
 
Dr. Philip de Groot
Wageningen University
 

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