<s>
Bayesian	B-General_Concept
tool	I-General_Concept
for	I-General_Concept
methylation	I-General_Concept
analysis	I-General_Concept
,	O
also	O
known	O
as	O
BATMAN	B-General_Concept
,	O
is	O
a	O
statistical	O
tool	O
for	O
analysing	O
methylated	O
DNA	O
immunoprecipitation	O
(	O
MeDIP	O
)	O
profiles	O
.	O
</s>
<s>
Therefore	O
,	O
to	O
get	O
the	O
full	O
picture	O
of	O
methylation	O
for	O
a	O
given	O
region	O
you	O
have	O
to	O
normalize	O
the	O
signal	O
you	O
get	O
from	O
the	O
MeDIP	O
experiment	O
to	O
the	O
number	O
of	O
CpGs	O
in	O
the	O
region	O
,	O
and	O
this	O
is	O
what	O
the	O
Batman	B-General_Concept
algorithm	O
does	O
.	O
</s>
<s>
Analysing	O
the	O
MeDIP	O
signal	O
of	O
the	O
above	O
example	O
would	O
give	O
Batman	B-General_Concept
scores	O
of	O
0.5	O
for	O
region	O
A	O
(	O
i.e.	O
</s>
<s>
In	O
this	O
way	O
Batman	B-General_Concept
converts	O
the	O
signals	O
from	O
MeDIP	O
experiments	O
to	O
absolute	O
methylation	O
levels	O
.	O
</s>
<s>
The	O
core	O
principle	O
of	O
the	O
Batman	B-General_Concept
algorithm	O
is	O
to	O
model	O
the	O
effects	O
of	O
varying	O
density	O
of	O
CpG	O
dinucleotides	O
,	O
and	O
the	O
effect	O
this	O
has	O
on	O
MeDIP	O
enrichment	O
of	O
DNA	O
fragments	O
.	O
</s>
<s>
The	O
basic	O
assumptions	O
of	O
Batman	B-General_Concept
:	O
</s>
<s>
Basic	O
parameters	O
in	O
Batman	B-General_Concept
:	O
</s>
<s>
In	O
Batman	B-General_Concept
model	O
,	O
the	O
complete	O
dataset	O
from	O
a	O
MeDIP/chip	O
experiment	O
,	O
A	O
,	O
can	O
be	O
represented	O
by	O
a	O
statistical	O
model	O
in	O
the	O
form	O
of	O
the	O
following	O
probability	O
distribution	O
:	O
</s>
<s>
To	O
solve	O
this	O
inference	O
problem	O
,	O
Batman	B-General_Concept
uses	O
nested	O
sampling	O
(	O
)	O
to	O
generate	O
100	O
independent	O
samples	O
from	O
f( m|A	O
)	O
for	O
each	O
tiled	O
region	O
of	O
the	O
genome	O
,	O
then	O
summarizes	O
the	O
most	O
likely	O
methylation	O
state	O
in	O
100-bp	O
windows	O
by	O
fitting	O
beta	O
distributions	O
to	O
these	O
samples	O
.	O
</s>
<s>
It	O
may	O
be	O
useful	O
to	O
take	O
the	O
following	O
points	O
into	O
account	O
when	O
considering	O
using	O
Batman	B-General_Concept
:	O
</s>
<s>
Batman	B-General_Concept
is	O
not	O
a	O
piece	O
of	O
software	O
;	O
it	O
is	O
an	O
algorithm	O
performed	O
using	O
the	O
command	O
prompt	O
.	O
</s>
<s>
Because	O
it	O
is	O
non-commercial	O
,	O
there	O
is	O
very	O
little	O
support	O
when	O
using	O
Batman	B-General_Concept
beyond	O
what	O
is	O
in	O
the	O
manual	O
.	O
</s>
<s>
(	O
Note	O
:	O
In	O
one	O
government	O
lab	O
,	O
running	O
Batman	B-General_Concept
on	O
a	O
set	O
of	O
100	O
Agilent	O
Human	O
DNA	O
Methylation	O
Arrays	O
(	O
about	O
250,000	O
probes	O
per	O
array	O
)	O
took	O
less	O
than	O
an	O
hour	O
to	O
complete	O
in	O
Agilent	O
's	O
Genomic	O
Workbench	O
software	O
.	O
</s>
<s>
One	O
of	O
the	O
basic	O
assumptions	O
of	O
Batman	B-General_Concept
is	O
that	O
all	O
DNA	O
methylation	O
occurs	O
at	O
CpG	O
dinucleotides	O
.	O
</s>
