Abstract
When testing a large number of hypotheses, estimating the proportion of true nulls, denoted by
, becomes increasingly important. This quantity has many applications in practice. For instance, a reliable estimate of
can eliminate the conservative bias of the Benjamini–Hochberg procedure on controlling the false discovery rate. It is known that most methods in the literature for estimating
are conservative. Recently, some attempts have been paid to reduce such estimation bias. Nevertheless, they are either over bias corrected or suffering from an unacceptably large estimation variance. In this paper, we propose a new method for estimating
that aims to reduce the bias and variance of the estimation simultaneously. To achieve this, we first utilize the probability density functions of false-null
-values and then propose a novel algorithm to estimate the quantity of
. The statistical behavior of the proposed estimator is also investigated. Finally, we carry out extensive simulation studies and several real data analysis to evaluate the performance of the proposed estimator. Both simulated and real data demonstrate that the proposed method may improve the existing literature significantly.
Keywords: Effect size, False-null p-value, Microarray data, Multiple testing, Probability density function, Upper tail probability
1. Introduction
When testing a large number of hypotheses, estimating the proportion of true nulls, denoted by
, becomes increasingly important. Studies using high-throughput techniques and microarray experiments that identify genes expressed differentially across groups, often involve testing hundreds or thousands of hypotheses simultaneously. In addition to identifying differentially expressed genes, we may also want to know the proportion of genes that are truly differentially expressed, i.e., the value of
. This quantity has many applications in practice. For instance, a reliable estimate of
can eliminate the conservative bias of the Benjamini–Hochberg procedure (Benjamini and Hochberg, 1995) on controlling the false discovery rate, and therefore increase the average power (Storey, 2002; Nguyen, 2004). A good estimate of
can also sharpen the Bonferroni-type family-wise error controlling procedures to improve the power and reduce the false negative rate (Hochberg and Benjamini, 1990; Finner and Gontscharuk, 2009). Besides the broad applications,
is also a quantity of interest that has its own right (Langaas and others, 2005).
The estimation of
was pioneered in Schweder and Spjtvoll (1982), where a graphical method was applied to evaluate a large number of tests on a plot of cumulative
-values using the observed significance probabilities. They claimed that the points on the graph corresponding to the true-null hypotheses should fall on a straight line and that this line can then be used to estimate
. Their method was further studied in Storey (2002) and Storey and others (2004). Since then, there is a rich body of literature on the estimation of
. For instance, Langaas and others (2005) proposed a new method for estimating
based on a nonparametric maximum likelihood estimation of the
-value density, subject to the restriction that the density is decreasing or convex decreasing. In general, their convex density estimator based on a convex decreasing density estimation outperforms other estimators with respect to the mean squared error (MSE). Other significant works in estimating
include: the smoothing spline method in Storey and Tibshirani (2003), the moment-based methods in Dalmasso and others (2005) and Lai (2007), the histogram methods in Nettleton and others (2006) and Tong and others (2013), the nonparametric method in Wu and others (2006), the average estimate method in Jiang and Doerge (2008), and the sliding linear model method in Wang and others (2011), among many others.
Assume that the test statistics are independent of each other. A straightforward model for the
-values is a two-component mixture model,
![]() |
(1.1) |
where the
-values under the null hypotheses follow the uniform distribution on
, and the
-values under the false-null hypotheses follow the distribution
. Due to the unidentifiability problem (Genovese and Wasserman, 2002; 2004), most existing methods aforementioned have targeted to estimate an identifiable upper bound of
, that is
. As a consequence, those estimators always overestimate
and we refer to them as conservative estimators. To obtain the identifiability in model (1.1), we need to make some assumptions on the density
. For instance, if
or if
has a parametric form, the model will be identifiable and so we can estimate
directly rather than the upper bound. Recently, some attempts have been made to the estimation of
, with a main focus on reducing the estimation bias (Pawitan and others, 2005; McLachlan and others, 2006; Ruppert and others, 2007; Qu and others, 2012). In particular, by assuming that absolute values of the noncentrality parameters (NCPs) from the false-null hypotheses follow a smooth distribution with density
, Ruppert and others (2007) developed a new methodology that combines a parametric model for the
-values given the NCPs and a nonparametric spline model for the NCPs. The quantity
and the coefficients in the spline model were then estimated by penalized least squares. In simulation studies, the authors demonstrated that their proposed estimator has the ability to reduce the bias in estimating
. More recently, their method was improved by Qu and others (2012) where the authors applied some new nonparametric and semiparametric methods to the estimation of the NCPs distribution. We refer to these estimators as bias-reduced estimators.
Though the existing bias-reduced estimators have significant merit in reducing the estimation bias, we note that the variations of these estimators are usually considerably enlarged. As reported in Tables 1 and 2 in Qu and others (2012), the interquartile ranges of their estimators are often more than twice as large as the other competitors. In addition, we observe that their estimators only perform well when the NCPs are concentrated around 0, i.e., when a majority of false nulls have very weak signals. In the situation of microarray data analysis, to make their estimators work a large proportion of false-null genes need to be weakly differentially expressed. Otherwise, their estimators tend to be over bias corrected (see Section 5 for more detail). In this paper, we propose a new method for estimating
that aims to reduce the bias and variance of the estimation simultaneously. To achieve this, we first utilize the probability density functions of false-null
-values and then propose a novel algorithm to estimate the quantity of
. Simulation studies will show that the proposed method may improve the existing literature significantly.
The rest of the paper is organized as follows. In Section 2, we introduce a bias-corrected method for estimating
that aims to reduce the bias and variance simultaneously. In Section 3, we derive the probability density functions of false-null
-values for testing two-sided hypotheses with unknown variances. In Section 4, we propose an algorithm for estimating
and investigate the behavior of the proposed estimator. We then evaluate the performance of the proposed estimator via extensive simulation studies in Section 5 and several microarray data sets in Section 6. Finally, we conclude the paper in Section 7 and provide the technical proofs in Appendices of supplementary material available at Biostatistics online.
2. Main results
Let
be the
-values corresponding to each of
total hypothesis tests. Let
(size
) denote the set of true-null hypotheses and
(size
) denote the set of false-null hypotheses. Then
and
. To avoid confusion, we define the “true-null
-values” as
-values from hypothesis tests in which the null was correct, and the “false-null
-values” as
-values from hypothesis tests in which the null was false. For a given
, define
to be the total number of
-values on
,
to be the total number of true-null
-values on
, and
to be the total number of false-null
-values on
. By definition, we have
. In addition, we have
since the true-null
-values are uniformly distributed in
. This suggests we estimate
by
![]() |
(2.1) |
However, (2.1) is not a valid estimator as
is unobservable in practice.
Note that the false-null
-values are more likely to be small. Thus for a reasonably large
, the majority of
-values on
should correspond to true-null
-values and so
. By this, Storey (2002) proposed to estimate
by
![]() |
(2.2) |
where
is the tuning parameter. We refer to
as the Storey estimator. For any
, it is easy to verify that
![]() |
This shows that
always overestimates
, and therefore, is a conservative estimator of
. The conservativeness of
can be rather significant when the sample size and/or the effect sizes of false-null hypotheses are small.
2.1. New methodology
We now propose a bias-corrected method for estimating
. For each false-null
-value with effect size
, let
be the probability density function and
be the upper tail probability on
. By the definition of
, we have
![]() |
(2.3) |
where
is the average upper tail probability for all false-null
-values. By (2.3) and the fact that
, we have
. This leads to
![]() |
(2.4) |
Let
be an estimate of
. By (2.4), we propose a new estimator of
as
![]() |
(2.5) |
Note that
is not guaranteed to be within
in practice. As in Storey (2002), we truncate
to
if
, and round
to
if
. This leads to the estimator to be
.
The term
serves as a regularization parameter of the proposed estimator. When
,
reduces to
. When
, in Appendix C of supplementary material available at Biostatistics online we show that
![]() |
for any
. That is, the proposed estimator is always less conservative than Storey’s estimator for any
. More discussion on
is given in Sections 3 and 4.
Finally, in addition to the bias elimination, we apply the average estimate method in Jiang and Doerge (2008) to further reduce the estimation variance. Specifically, let
where
and
is an integer value. We then compute
for each
and take their average as the final estimate,
![]() |
(2.6) |
where
is the number of
contained in the set
. We note that the average estimate method is very robust when the independence assumption is violated.
2.2. Choice of the set
Needless to say, the set
may play an important role for the proposed estimator. In what follows we investigate the choice of an appropriate set
in practice. Recall that for the estimator
in (2.2), there is a severe bias-variance trade-off on the tuning parameter
. Specifically, (i) when
, the variance of
is smaller but the bias increases; and (ii) when
, the bias of
is smaller but the variance increases. In practice, the optimal
is suggested to be the one that minimizes the MSE and is implemented by a bootstrap procedure in Storey and others (2004).
We note that, unlike the Storey estimator
, the proposed estimator
in (2.5) has little bias and does not suffer a severe bias-variance trade-off along with the choice of
. Thus, to choose an appropriate
value, we can aim to minimize the variance of the estimator only. Simulations (not shown) indicate that the variance of
is usually larger when
is near 0 or 1 than when it is near the middle of the range. In addition, from a theoretical point of view, we found that
for the proposed
in Section 4.1. Recall that
is the denominator of (2.5). This implies that
may not be stable and may have a large variation when
is near 0 or 1. That is, to make
a good estimate the
value should not be too small or large. In Appendix D of supplementary material available at Biostatistics online, a simulation study is conducted that investigates how sensitive the method is to the choice of boundaries
,
and
. According to the simulation results, we apply the set
throughout the paper.
3. Probability density function of false-null
-values
Given the set
, to implement the estimator (2.6) we need to have an appropriate estimate for the unknown quantity
. To achieve this, we need to have the probability density functions
for each false-null
-value with effect size
, where
. For ease of notation, in this section we will not specify the subscript
in effect sizes unless otherwise specified. Our aim is then to determine the probability density function
of a false-null
-value with effect size
.
For the one-sample comparison, let
be a random sample of size
from a normal distribution with mean
and variance
. Let
be the sample mean,
be the sample variance, and
be the effect size. For testing the one-sided hypothesis
![]() |
(3.1) |
Hung and others (1997) assumed a known
and considered the test statistic
. Under
, the test statistic
follows a standard normal distribution. This yields a
-value of
, where
is the realization of
and
is the probability function of the standard normal distribution. Under
,
is normally distributed with mean
and variance
. Then, by Jacobian transformation, for given
and
the probability density function of
is
![]() |
(3.2) |
where
is the
th percentile of the standard normal distribution. Further, we have
![]() |
(3.3) |
Needless to say, the assumption of known variances and also the restriction to one-sided tests in Hung and others (1997) limited its application in testing the differential expression of genes. The small sample size in such studies can be another concern. Hence, to accommodate the needs of microarray studies, we extend their method to the two-sided testing problems with unknown variances.
3.1. Two-sided tests with unknown variances
We first consider the one-sample, two-sided comparison. For testing the hypothesis
![]() |
(3.4) |
We consider the test statistic
, where
and
are the sample mean and sample variance, respectively. Let
be the effect size. Under
, the test statistic
follows a Student’s
distribution with
degrees of freedom.
The
-value for testing (3.4) is given as
, where
is the realization of
,
and
is the probability function of Student’s
distribution with
degrees of freedom. Under
, it is easy to verify that
follows a non-central
distribution with
degrees of freedom and NCP
. Let
be the
th percentile of Student’s
distribution with
degrees of freedom. In Appendix B of supplementary material available at Biostatistics online, for any given
and
, we show that the probability density function of
is
![]() |
(3.5) |
where
is the probability density function of Student’s
distribution with
degrees of freedom, and
is the probability density function of the non-central
distribution with
degrees of freedom and NCP
. When
, both
and
reduce to
so that
follows a uniform distribution in
. When
, we have
![]() |
(3.6) |
where
is the probability function of the non-central
distribution with
degrees of freedom and NCP
.
Now we consider the two-sample, two-sided comparison. Let
be a random sample of size
from the normal distribution with mean
and variance
, and
be a random sample of size
from the normal distribution with mean
and variance
. Let also
and
be the sample means for the two samples, respectively. For testing the hypothesis
![]() |
(3.7) |
we consider the test statistic
, where
is the pooled sample variance with
and
. Under
,
follows a Student’s
distribution with
degrees of freedom. Under
,
follows a non-central
distribution with
degrees of freedom and NCP
. Thus to make formulas (3.5) and (3.6) applicable to the two-sample comparison, we only need to redefine
,
and
as follows:
,
and
. Finally, if a common variance in (3.7) is not assumed, we may apply Welch’s
-test statistic and it follows an approximate
distribution.
4. The proposed algorithm for estimating
For the one-sample comparison, an intuitive estimator of
is given as
, where
is the sample mean and
is the sample standard deviation. However,
is suboptimal as it is biased. Alternatively, because
and
are independent of each other, we have
![]() |
(4.1) |
where
follows an inverse-
distribution with
degrees of freedom,
, and
is the gamma function. By (4.1), an unbiased estimator of
is given as
![]() |
(4.2) |
Similarly, for the two-sample comparison, an unbiased estimator of
is
![]() |
(4.3) |
where
is the pooled sample variance.
4.1. Algorithm for estimating
For the sake of brevity, we present in this section the estimation procedure for the one-sample, two-sided comparison only. Note that the procedure is generally applicable when estimating
in other settings. The proposed algorithm for estimating
is as follows.
For each
, we estimate
by the unbiased estimator
in (4.2).- For each
and
, we estimate the upper tail probability
by
We then order the values of
(4.4)
for each
such that

- Let
, where
is an initial estimate of
and
is the integral part of
. Then for each
, we estimate the average upper tail probability
by

(4.5) - Given the estimates
for all
, we estimate
by

(4.6)
We note that the initial estimate of
may play an important role for the proposed estimation procedure. When the initial estimate
is too large,
tends to be small and so is
. As a consequence, the bias correction of
over
may not be observable. On the other hand, when the initial estimate
is too small, it may result in an over bias-corrected estimate. In Appendix E of supplementary material available at Biostatistics online, a simulation study is conducted that investigates how sensitive the method is to the choice of the initial estimator of
. According to the simulation results, we adopt the bootstrap estimator
in Storey and others (2004) as the initial estimate of
in the proposed algorithm.
4.2. Behavior of the proposed estimator
The following result shows that the proposed estimator is always less conservative than the estimator of Jiang and Doerge (2008).
Theorem 1 —
For any given
set
, the proposed
in (4.6) is a less conservative estimator of
than the average estimate
in Jiang and Doerge (2008), where
(4.7)
The proof of Theorem 1 is given in Appendix C of supplementary material available at Biostatistics online. In addition, under certain conditions we can show that
is asymptotically larger than
so that the bias of
is not over corrected. Specifically, we assume that (i) the initial estimate
; and (ii)
is a random sample from a certain distribution with a finite second moment. By (i), we have
and so
![]() |
By (ii) and by the strong law of large numbers, we have
as
. Alternatively if the sample size
, by (4.2) we have
and
. Then for any fixed
,
as
. This shows that the proposed estimator protects from over bias correction and so is an asymptotically conservative estimator. In this sense, the proposed estimator improved the bias-reduced estimators in Ruppert and others (2007) and Qu and others (2012). Finally, we hope to clarify that the assumptions made above are very strong and may not hold in practice. Further research is warranted to investigate the statistical properties of the proposed estimator.
5. Simulation studies
In this section, we conduct simulation studies to assess the performance of the proposed estimator under various simulation settings. The five estimators we adopt for comparison are (i) the bootstrap estimator
in Storey and others (2004), (ii) the average estimate estimator
in Jiang and Doerge (2008), (iii) the convex estimator
in Langaas and others (2005), (iv) the parametric estimator
in Qu and others (2012) and (v) the proposed estimator
.
5.1. Simulation setup
Consider a microarray experiment with
genes and
arrays. In this study, we set
and consider
and
. The
-dimensional arrays are generated from a multivariate normal distribution with mean vector
and covariance matrix
. To mimic a realistic scenario, we assume that the covariance matrix is a block diagonal matrix such that
![]() |
where
and
follows an auto-regressive structure. Let
throughout the simulation studies. We consider four different values of
, ranging from 0, 0.4 to 0.8, to represent different levels of dependence. Note that
corresponds to a diagonal matrix and so is the situation where all the genes are independent of each other. Finally, we simulate
independent and identically distributed (i.i.d) from the distribution
to account for the heterogeneity of variance in genes.
The next step is to split the
genes with
constant genes corresponding to the true-null hypotheses, and
differential expressed genes corresponding to the false-null hypotheses. To achieve this, we first randomly sample a set of
numbers, denoted by
, from the integer set
. Let
be the complement set so that
. We then assign
for each
, and simulate
i.i.d. from the uniform distribution on the interval
for each
. In other words, we specify the mean vector as
. For a complete comparison, we consider 9 values of
, ranging from
,
to
, to represent different levels of proportion of true-null hypotheses.
For each combination of
and
, we first generate
and
using the algorithm specified above. We then simulate the
arrays
,
, independently from the multivariate normal distribution with the generated mean
and covariance matrix
. To test the hypotheses
versus
, we let
, where
and
are the sample mean and sample standard deviation of gene
, respectively. We then compute the
-values as
, with
the realization of
, and estimate the estimators
,
,
and
using the computed
-values.
5.2. Simulation results
Following the above procedure, we simulate
sets of independent data for each combination setting of
. For each method, we compute the MSE as
![]() |
where
is the estimated
for the
th simulated data set and
is the sample average. We report the MSEs of the five estimators as functions of the true
in Figure 1 for
and
and
,
and
, respectively. It is evident that the proposed
provides a smaller MSE than the other four estimators in most settings. Specifically, we note that (i) for small and moderate
values, the proposed
is always the best estimator and (ii) for large
values, the proposed
is in a league with
and
that provide the best performance. We note that the comparison results among
,
, and
remain similar to those reported in Langaas and others (2005) and Jiang and Doerge (2008). In addition, the estimator
is always suboptimal throughout the simulations.
Figure 1.
Plots of MSEs as functions of
for various
and
values, where “1” represents the bootstrap estimator
, “2” represents the average estimate estimator
, “3” represents the convex estimator
, “4” represents the parametric estimator
, and “5” represents the proposed new estimator
.
To visualize how the proposed method improves the existing methods, we plot the density estimates of the distributions of the estimators in Figure 2 for
and in Figure 3 for
. To save space, we only present the results for
,
and
and
and
; the comparison patterns for other combination settings remain similar. From the densities, we note that (i) for small
values such as
, the proposed
provides to be an unbiased estimator or a slightly underestimated estimator, whereas
underestimates
and the other three overestimate
; (ii) for moderate
values such as
, the proposed
proves to be an unbiased estimator or slightly overestimates
, whereas the other four estimators keep the pattern as that for
; and (iii) for large
values such as
, all five estimators tend to have a small bias, whereas
and
perform worst due to the large variability in the estimation. In addition,
and
perform very similarly for
no matter what values of
and
are used. Finally, it is noteworthy that we have also conducted simulation studies for larger
values and the comparison results remain similar. For more details, please refer to Appendix F of supplementary material available at Biostatistics online.
Figure 2.
Density estimates of
for
, where the short dashed line represents the bootstrap estimator
, the dash-dotted line represents the average estimate estimator
, the dotted line represents the convex estimator
, the long dashed line represents the parametric estimator
, and the solid line represents the proposed new estimator
.
Figure 3.
Density estimates of
for
, where the short dashed line represents the bootstrap estimator
, the dash-dotted line represents the average estimate estimator
, the dotted line represents the convex estimator
, the long dashed line represents the parametric estimator
, and the solid line represents the proposed new estimator
.
6. Applications to Microarray data
In this section, we apply the proposed estimator to several microarray data sets for estimating
. The first data set is from the experiment described by Kuo and others (2003). The objective of the experiment was to identify the targets of the Arf gene on the Arf-Mdm2-p53 tumor suppressor pathway. In this study, the cDNA microarrays were printed from a murine clone library available at St. Jude Children’s Research Hospital. Samples from reference and Arf-induced cell lines were taken at 0, 2, 4 and 8 h. At each time point, three independent replicates of cDNA microarray were generated. There were 5776 probe spots on each array. Only 2936 spots that passed a quality control of image analysis were used for differential expression analysis. The
-values used in the study were generated by Pounds and Cheng (2004) where
-values were computed by permutation tests (see Figure 4A for the histogram of the
-values). The second data set is the Estrogen data and is described in the “Estrogen 2x2 Factorial Design” vignette by Scholtens and others (2004). The objective of the study was to investigate the effect of estrogen on the genes in ER
breast cancer cells over time. The
-values of testing null hypothesis of no differential expression in the presence and absence of estrogen were used in our study (see Figure 4B for the histogram of the
-values). The third data set is the cancer cell line experiment described by Cui and others (2005). The data set is from a cDNA microarray experiment and the objective is to identify differentially expressed genes in two human colon cancer cell lines, CACO2 and HCT116, and three human ovarian cancer cell lines, ES2, MDAH2774 and OV1063. In total, there were
genes tested on each array. The
-values of testing differential expression among these cell lines were then generated by fitting an analysis of variance model to each gene to account for the multiple sources of variation including array, dye and sample effects (see Figure 4C for the histogram of the
-values).
Figure 4.

Histograms of
-values for the three data sets, where (A), (B), and (C) correspond to the
-values for the first, second, and third data set, respectively.
Table 1 reports the estimated values of
for the three data sets using the bootstrap estimator
, the average estimate estimator
, the convex estimator
and the proposed estimator
, respectively. Note that the parametric estimator
in Qu and others (2012) is not reported because the two-sided
-statistics are not available for these data sets. Among the four estimators, we observe that
is smaller than the other three estimators in most cases, especially for
. This is consistent with the conclusion in Theorem 1. For the first data set,
is the smallest and is followed by
and
, whereas
is far above them. For the second data set, there is a high degree of agreement among the estimators except for
which is much larger. For the third data set,
is similar to
and
and is less conservative compared with
.
Table 1.
Estimation of
for the three data sets using the bootstrap estimator
the average estimate estimator
the convex estimator
and the proposed estimator
respectively.
| Data Set 1 | Data Set 2 | Data Set 3 | |
|---|---|---|---|
![]() |
0.447 | 0.944 | 0.486 |
![]() |
0.658 | 0.884 | 0.583 |
![]() |
0.463 | 0.875 | 0.501 |
![]() |
0.431 | 0.877 | 0.498 |
7. Conclusion
The proportion of true-null hypotheses,
, is an important quantity in multiple testing and has attracted a lot of attention in the recent literature. It is known that most existing methods for estimating
are either too conservative or suffering from an unacceptably large estimation variance. In this paper, we propose a new method for estimating
that reduces the bias and variance of the estimation simultaneously. To achieve this, we first utilize the probability density functions of false-null
-values and then propose a novel algorithm to estimate the quantity of
. The statistical behavior of the proposed estimator is also investigated. Through extensive simulation studies and real data analysis, we demonstrated that the proposed estimator may substantially decrease the bias and variance compared to most existing competitors, and therefore, improve the existing literature significantly. Finally, we note that the paper has focused on the estimation of
only. Some related questions, such as the behavior of false discovery rate using the proposed estimator, may warrant further studies.
Supplementary material
Supplementary Material is available at http://biostatistics.oxfordjournals.org.
Acknowledgements
Yebin Cheng’s research was supported in part by National Natural Science Foundation of China grant No.11271241) and Shanghai Leading Academic Discipline Project No.863. Dexiang Gao’s research was supported in part by NIH grant R01 CA 157850-02 and 51P30 CA46934. Tiejun Tong’s research was supported in part by Hong Kong Research grant HKBU202711 and Hong Kong Baptist University FRG grants FRG2/11-12/110 and FRG1/13-14/018. The authors thank the editor, the associate editor, a referee and Bryan McNair for their constructive comments that led to a substantial improvement of the paper. Conflict of Interest: None declared.
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