Biomedical Engineering Reference
In-Depth Information
generated by complicated normalization, rank is a simple measure using
intensity order.
2.2.2. The Use of PM
Aymetrix oligonucleotide gene chips use a set of pairs of probes to in-
terrogate a given gene. Each pair consists of a perfect match probe (PM)
and a mismatch probe (MM). PM is used to detect mRNA concentration
of a target gene whereas MM is designed to identify background intensity
and cross-hybridization. Here we consider only PM probe level data be-
cause of potential biases introduced by the use of MM. For example, PM
is contaminated with background and cross-hybridization, so PM intensity
is supposed to be greater than MM intensity. However, it is common to see
a substantial portion of probe pairs with MM>PM (30%50%) and a
high correlation between PM and MM
30
. Such patterns suggest MM also
partially measures RNA concentration. Subtraction of MM from PM likely
underestimates mRNA concentration. Thus, we consider PM intensity for
data analysis. We dene PM rank as the rank of PM intensity over all
probes in the gene chip. Below we describe a rank approach (un-weighted),
and a weighted rank approach
63;64
.
2.2.3. Probe Rank Approach
Let Y
i;j;k
be a PM rank for the jth probe in the ith gene on array k. Assume
group A has arrays a
1
; a
2
; : : : ; a
n
1
and group B has arrays b
1
; b
2
; : : : ; b
n
2
(e.g., treatment versus control groups). Consider a dierence of two per-
centiles from the two groups.
D
(i;j)
A;B
= (P
a
th percentile of S
a
P
b
th percentile of S
b
)=n;
where S
a
=fY
(i;j;a
1
)
; : : : ; Y
(i;j;a
n1
)
g, Sb =fY
(i;j;b
1
)
; : : : ; Y
(i;j;b
n2
)
g, and n
represents the total number of probes in an array (e.g., there are 201,807
probes in a HG-u95A gene chip). P
a
could be 0 (i.e., the minimum), and
P
b
could be 100 (i.e., the maximum) when sample size is small (e.g., 2 or
3 in vitro study). D
(i;j)
A;B
is a measure of dierence between group A and
group B. The measure between group B and group A is dened similarly.
Denote the number of probes for gene i as J
i
. A gene i is considered to be
an altered gene if
1
J
i
P
J
i
j=1
I(D
(i;j)
> P
(i)
probe;(A;B)
)P
(i)
gene;(A;B)
or
A;B
P
J
i
j=1
I(D
(i;j)
B;A
> P
(i)
probe;(B;A)
)P
(i)
1
J
i
gene;(B;A)
,
where P
(i)
probe;E
represents a probe level threshold with E as (A; B) or (B; A),
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