<s>
lumi	B-Application
is	O
a	O
free	B-Application
,	O
open	B-Application
source	I-Application
and	O
open	O
development	O
software	O
project	O
for	O
the	O
analysis	O
and	O
comprehension	O
of	O
Illumina	O
expression	O
and	O
methylation	O
microarray	O
data	O
.	O
</s>
<s>
The	O
project	O
was	O
started	O
in	O
the	O
summer	O
of	O
2006	O
and	O
set	O
out	O
to	O
provide	O
algorithms	O
and	O
data	O
management	O
tools	O
of	O
Illumina	O
in	O
the	O
framework	O
of	O
Bioconductor	B-Application
.	O
</s>
<s>
It	O
is	O
based	O
on	O
the	O
statistical	O
R	B-Language
programming	I-Language
language	I-Language
.	O
</s>
<s>
The	O
lumi	B-Application
package	O
provides	O
an	O
analysis	O
pipeline	O
for	O
probe-level	O
Illumina	O
expression	O
and	O
methylation	O
microarray	O
data	O
,	O
including	O
probe-identifier	O
management	O
(	O
nuID	O
)	O
,	O
updated	O
probe-to-gene	O
mapping	O
and	O
annotation	O
using	O
the	O
latest	O
release	O
of	O
RefSeq	O
(	O
nuIDblast	O
)	O
,	O
probe-intensity	O
transformation	O
(	O
VST	O
)	O
and	O
normalization	O
(	O
RSN	O
)	O
,	O
quality	O
control	O
(	O
QA/QC	O
)	O
and	O
preprocessing	O
methods	O
specific	O
for	O
Illumina	O
methylation	O
data	O
.	O
</s>
<s>
By	O
extending	O
the	O
ExprSet	O
object	O
with	O
Illumina-specific	O
features	O
,	O
lumi	B-Application
is	O
designed	O
to	O
work	O
with	O
other	O
Bioconductor	B-Application
packages	O
,	O
such	O
as	O
Limma	O
and	O
GOstats	O
to	O
detect	O
differential	O
genes	O
and	O
conduct	O
Gene	O
Ontology	O
analysis	O
.	O
</s>
<s>
The	O
lumi	B-Application
project	O
was	O
started	O
in	O
the	O
summer	O
of	O
2006	O
at	O
the	O
Bioinformatics	O
Core	O
Facility	O
of	O
the	O
Robert	O
H	O
.	O
Lurie	O
Comprehensive	O
Cancer	O
Center	O
,	O
Northwestern	O
University	O
.	O
</s>
<s>
Originally	O
lumi	B-Application
was	O
designed	O
for	O
the	O
analysis	O
of	O
Illumina	O
Expression	O
BeadArray	O
data	O
.	O
</s>
<s>
lumi	B-Application
was	O
the	O
first	O
software	O
package	O
to	O
utilize	O
the	O
unique	O
design	O
of	O
redundancy	O
of	O
beadArrays	O
for	O
the	O
data	O
transformation	O
and	O
normalization	O
processes	O
.	O
</s>
<s>
The	O
first	O
release	O
of	O
lumi	B-Application
was	O
on	O
January	O
3	O
,	O
2007	O
through	O
the	O
Bioconductor	B-Application
website	O
.	O
</s>
