44. Distance
Metrics
• Correla<on
– maximum
value
of
1
if
X
and
Y
are
perfectly
correlated
– minimum
value
of
-‐1
if
X
and
Y
are
exactly
opposite
– d(X,Y)
=
1
–
rxy
• Many,
many
others
• Choice
of
distance
metric
can
be
driven
by
underlying
data
(eg.,
binary
data,
categorical
data,
outliers,
etc.)
67. Experimental
Design
• What
are
my
goals?
– Differen<al
expression?
– Transcriptome
assembly?
– Iden<fy
rare,
novel
trancripts?
• System
characteris<cs?
– Large,
expanded
genome?
– Intron/exon
structures
complex?
– No
reference
genome
or
transcriptome
68. Experimental
Design
• Technical
replicates
– Probably
not
needed
due
to
low
technical
varia<on
• Biological
replicates
– Not
explicitly
needed
for
transcript
assembly
– Essen<al
for
differen<al
expression
analysis
– Number
of
replicates
oaen
driven
by
sample
availability
for
human
studies
– More
is
almost
always
beger