<s>
Microarray	B-Algorithm
analysis	I-Algorithm
techniques	I-Algorithm
are	O
used	O
in	O
interpreting	O
the	O
data	O
generated	O
from	O
experiments	O
on	O
DNA	O
(	O
Gene	B-Algorithm
chip	I-Algorithm
analysis	I-Algorithm
)	O
,	O
RNA	O
,	O
and	O
protein	O
microarrays	O
,	O
which	O
allow	O
researchers	O
to	O
investigate	O
the	O
expression	O
state	O
of	O
a	O
large	O
number	O
of	O
genes	O
-	O
in	O
many	O
cases	O
,	O
an	O
organism	O
's	O
entire	O
genome	O
-	O
in	O
a	O
single	O
experiment	O
.	O
</s>
<s>
MA	O
plots	O
can	O
be	O
produced	O
using	O
programs	O
and	O
languages	O
such	O
as	O
R	B-Language
,	O
MATLAB	O
,	O
and	O
Excel	O
.	O
</s>
<s>
Robust	O
Multi-array	O
Average	O
(	O
RMA	O
)	O
is	O
a	O
normalization	O
approach	O
that	O
does	O
not	O
take	O
advantage	O
of	O
these	O
mismatch	O
spots	O
,	O
but	O
still	O
must	O
summarize	O
the	O
perfect	O
matches	O
through	O
median	B-General_Concept
polish	I-General_Concept
.	O
</s>
<s>
The	O
median	B-General_Concept
polish	I-General_Concept
algorithm	O
,	O
although	O
robust	O
,	O
behaves	O
differently	O
depending	O
on	O
the	O
number	O
of	O
samples	O
analyzed	O
.	O
</s>
<s>
More	O
sophisticated	O
approaches	O
are	O
often	O
related	O
to	O
t-tests	B-General_Concept
or	O
other	O
mechanisms	O
that	O
take	O
both	O
effect	O
size	O
and	O
variability	O
into	O
account	O
.	O
</s>
<s>
Hierarchical	B-Algorithm
clustering	I-Algorithm
,	O
and	O
k-means	B-Algorithm
clustering	I-Algorithm
are	O
widely	O
used	O
techniques	O
in	O
microarray	O
analysis	O
.	O
</s>
<s>
Hierarchical	B-Algorithm
clustering	I-Algorithm
is	O
a	O
statistical	O
method	O
for	O
finding	O
relatively	O
homogeneous	O
clusters	O
.	O
</s>
<s>
Hierarchical	B-Algorithm
clustering	I-Algorithm
consists	O
of	O
two	O
separate	O
phases	O
.	O
</s>
<s>
Pearson	O
's	O
correlation	O
and	O
Spearman	B-General_Concept
's	I-General_Concept
correlation	I-General_Concept
are	O
often	O
used	O
as	O
dissimilarity	O
estimates	O
,	O
but	O
other	O
methods	O
,	O
like	O
Manhattan	O
distance	O
or	O
Euclidean	O
distance	O
,	O
can	O
also	O
be	O
applied	O
.	O
</s>
<s>
After	O
calculation	O
of	O
the	O
initial	O
distance	O
matrix	O
,	O
the	O
hierarchical	B-Algorithm
clustering	I-Algorithm
algorithm	O
either	O
(	O
A	O
)	O
joins	O
iteratively	O
the	O
two	O
closest	O
clusters	O
starting	O
from	O
single	O
data	O
points	O
(	O
agglomerative	O
,	O
bottom-up	O
approach	O
,	O
which	O
is	O
fairly	O
more	O
commonly	O
used	O
)	O
,	O
or	O
(	O
B	O
)	O
partitions	O
clusters	O
iteratively	O
starting	O
from	O
the	O
complete	O
set	O
(	O
divisive	O
,	O
top-down	O
approach	O
)	O
.	O
</s>
<s>
Hierarchical	B-Algorithm
cluster	I-Algorithm
analysis	I-Algorithm
methods	O
include	O
:	O
</s>
<s>
Average	O
linkage	O
(	O
UPGMA	B-Algorithm
)	O
.	O
</s>
<s>
K-means	B-Algorithm
clustering	I-Algorithm
is	O
an	O
algorithm	O
for	O
grouping	O
genes	O
or	O
samples	O
based	O
on	O
pattern	O
into	O
K	O
groups	O
.	O
</s>
<s>
Thus	O
the	O
purpose	O
of	O
K-means	B-Algorithm
clustering	I-Algorithm
is	O
to	O
classify	O
data	O
based	O
on	O
similar	O
expression	O
.	O
</s>
<s>
K-means	B-Algorithm
clustering	I-Algorithm
algorithm	I-Algorithm
and	O
some	O
of	O
its	O
variants	O
(	O
including	O
k-medoids	B-Algorithm
)	O
have	O
been	O
shown	O
to	O
produce	O
good	O
results	O
for	O
gene	O
expression	O
data	O
(	O
at	O
least	O
better	O
than	O
hierarchical	B-Algorithm
clustering	I-Algorithm
methods	O
)	O
.	O
</s>
<s>
Empirical	O
comparisons	O
of	O
k-means	B-Algorithm
,	O
k-medoids	B-Algorithm
,	O
hierarchical	O
methods	O
and	O
,	O
different	O
distance	O
measures	O
can	O
be	O
found	O
in	O
the	O
literature	O
.	O
</s>
<s>
Non-commercial	O
tools	O
such	O
as	O
FunRich	O
,	O
GenMAPP	B-Application
and	O
Moksiskaan	O
also	O
aid	O
in	O
organizing	O
and	O
visualizing	O
gene	O
network	O
data	O
procured	O
from	O
one	O
or	O
several	O
microarray	O
experiments	O
.	O
</s>
<s>
A	O
wide	O
variety	O
of	O
microarray	O
analysis	O
tools	O
are	O
available	O
through	O
Bioconductor	B-Application
written	O
in	O
the	O
R	B-Language
programming	I-Language
language	I-Language
.	O
</s>
<s>
One	O
such	O
method	O
of	O
analysis	O
,	O
known	O
as	O
Gene	O
Set	O
Enrichment	O
Analysis	O
(	O
GSEA	O
)	O
,	O
uses	O
a	O
Kolmogorov-Smirnov-style	O
statistic	O
to	O
identify	O
groups	O
of	O
genes	O
that	O
are	O
regulated	O
together	O
.	O
</s>
<s>
Genevestigator	B-Application
is	O
a	O
public	O
tool	O
to	O
perform	O
contextual	O
meta-analysis	O
across	O
contexts	O
such	O
as	O
anatomical	O
parts	O
,	O
stages	O
of	O
development	O
,	O
and	O
response	O
to	O
diseases	O
,	O
chemicals	O
,	O
stresses	O
,	O
and	O
neoplasms	O
.	O
</s>
<s>
SAM	O
is	O
distributed	O
by	O
Stanford	O
University	O
in	O
an	O
R-package	B-Language
.	O
</s>
<s>
SAM	O
identifies	O
statistically	O
significant	O
genes	O
by	O
carrying	O
out	O
gene	O
specific	O
t-tests	B-General_Concept
and	O
computes	O
a	O
statistic	O
dj	O
for	O
each	O
gene	O
j	O
,	O
which	O
measures	O
the	O
strength	O
of	O
the	O
relationship	O
between	O
gene	O
expression	O
and	O
a	O
response	O
variable	O
.	O
</s>
<s>
This	O
analysis	O
uses	O
non-parametric	B-General_Concept
statistics	I-General_Concept
,	O
since	O
the	O
data	O
may	O
not	O
follow	O
a	O
normal	O
distribution	O
.	O
</s>
<s>
In	O
this	O
method	O
,	O
repeated	O
permutations	B-Algorithm
of	O
the	O
data	O
are	O
used	O
to	O
determine	O
if	O
the	O
expression	O
of	O
any	O
gene	O
is	O
significant	O
related	O
to	O
the	O
response	O
.	O
</s>
<s>
The	O
use	O
of	O
permutation-based	O
analysis	O
accounts	O
for	O
correlations	O
in	O
genes	O
and	O
avoids	O
parametric	O
assumptions	O
about	O
the	O
distribution	O
of	O
individual	O
genes	O
.	O
</s>
<s>
This	O
is	O
an	O
advantage	O
over	O
other	O
techniques	O
(	O
e.g.	O
,	O
ANOVA	B-General_Concept
and	O
Bonferroni	O
)	O
,	O
which	O
assume	O
equal	O
variance	O
and/or	O
independence	O
of	O
genes	O
.	O
</s>
<s>
Blocks	O
are	O
batches	O
of	O
microarrays	O
;	O
for	O
example	O
for	O
eight	O
samples	O
split	O
into	O
two	O
groups	O
(	O
control	O
and	O
affected	O
)	O
there	O
are	O
4	O
!=	O
24	O
permutations	B-Algorithm
for	O
each	O
block	O
and	O
the	O
total	O
number	O
of	O
permutations	B-Algorithm
is	O
(	O
24	O
)	O
(	O
24	O
)	O
=	O
576	O
.	O
</s>
<s>
A	O
minimum	O
of	O
1000	O
permutations	B-Algorithm
are	O
recommended	O
;	O
</s>
<s>
SAM	O
calculates	O
a	O
test	O
statistic	O
for	O
relative	O
difference	O
in	O
gene	O
expression	O
based	O
on	O
permutation	B-Algorithm
analysis	O
of	O
expression	O
data	O
and	O
calculates	O
a	O
false	O
discovery	O
rate	O
.	O
</s>
