Question: Q-values way smaller than P-values! Is that kosher?

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Joshua Banta •

**30**wrote:Dear listserv,
Consider the following vector of P-values:
p.values <- c(
0.266845129,
0.353675275,
0.030585143,
0.791285527,
0.60805832,
0.433466716,
0.039369439,
0.48918122,
0.740626586
)
When I run the qvalue function of the qvalue package, I get a rather
surprising outcome: the q-values are much smaller than the
corresponding p-values!
See the following code below:
source("http://bioconductor.org/biocLite.R")
biocLite("qvalue")
library(qvalue)
q.values <- qvalue(p.values)$qvalue
comparison <- cbind(p.values, q.values)
colnames(comparison) <- c("p.values", "q.values")
comparison
p.values q.values
[1,] 0.26684513 0.037111560
[2,] 0.35367528 0.037111560
[3,] 0.03058514 0.008960246
[4,] 0.79128553 0.040020397
[5,] 0.60805832 0.039540110
[6,] 0.43346672 0.037111560
[7,] 0.03936944 0.008960246
[8,] 0.48918122 0.037111560
[9,] 0.74062659 0.040020397
So what is happening here? Can I trust the q-values? In each case they
are substantially larger than the P-values. Especially troubling to me
are rows 4, 5, and 9.
Thanks in advance for any information/advice!
-----------------------------------
Josh Banta, Ph.D
Assistant Professor
Department of Biology
The University of Texas at Tyler
Tyler, TX 75799
Tel: (903) 565-5655
http://plantevolutionaryecology.org
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modified 4.7 years ago
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Michael Love ♦

**19k**• written 4.7 years ago by Joshua Banta •**30**