Statistics and Data Analysis for Microarrays Using R and Bioconductor, 2nd Edition

Pathway analysis 923

pathway impact analysis can still be used to assess the impact of a condition on

specific pathways. This is achieved by setting all measured expression changes

∆E(g ) = 0 for a ll genes on the given pathway g ∈ P

i

. This will make all gene

perturbation factors zer o:

P F (g) = ∆E(g) +

X

u∈US

g

β

ug

·

P F (u)

N

ds

(u)

= 0 (28.31)

Assuming that there are at least some differentially expressed genes somewhere

in this data set,

3

(i.e.,

|∆E| 6= 0), the pathway impact factor in Eq. 28.18

becomes:

IF (P

i

) = log



1

p

i



+

P

g∈P

i

|P F (g)|

|∆E|· N

de

(P

i

)

= log



1

p

i



+ 0 = −log(p

i

) (28.32)

Since the expression now involves a single random variable, the IF values will ...