I think this is kind of a stupid question but I cant get it right so I will
risk my hide.

 

# First I do a topTable as usual, but without adjustment for multiple
testing.

topt.dc <-
topTable(fit=ebobj,number=length(ebobj$coef),adjust.method="none",sort.by="t
")

 

> topt.dc[1:3,]

              M          A         t      P.Value         B

20861 -1.025634 -1.0256342 -14.87215 1.285609e-10 13.716847

680   -1.889194 -1.8891945 -14.58354 1.711049e-10 13.493043

24876 -1.861192 -1.8611920 -14.30543 2.264364e-10 13.271669

 

# The degrees of freedom for the moderated t-test is if I am not mistaken

df.dc <- ebobj$df.prior + ebobj$df.residual

 

# If you look at the toptable the P-value for the first gene is 1.285609e-10
and the t-value is -14.87215.

 

# but if I try to get the t-value from the p-value by

qt(p=topt.dc[1,4], df=df.dc[idx.vec[1]],lower.tail = TRUE)

-14.18081


#which differs from -14.87215. The difference is bigger for the second gene.


# -13.9039 vs -14.58354

 

What am I doing wrong?

 

Best regards

 

// Johan Lindberg

 

****************************************************************************
***************

Johan Lindberg

Royal Institute of Technology

AlbaNova University Center

Stockholm Center for Physics, Astronomy and Biotechnology

School of Molecular Biotechnology

Department of Gene Technology

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Roslagstullsbacken 21, Floor 3

106 91 Stockholm, Sweden

Delivering address:

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104 06 Stockholm, Sweden

Phone (office) +46 8 553 783 44

Fax + 46 8 553 784 81

 <http://www.ktharray.se/> http://www.ktharray.se/

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