...
Important
...
update
...
(January
...
20th,
...
2011):
...
the
...
data
...
below
...
have
...
been
...
corrected
...
for
...
the
...
BCR
...
batch
...
which
...
is
...
not
...
necessarily
...
the
...
processing
...
batch.
...
The
...
dataset
...
needs
...
to
...
be
...
reanalyzed.
...
Correlation between BCR batch and the processing batch for 27k arrays (January 20, 2012):
| Wiki Markup |
|---|
{csv}Batch on the download page,"# after ""HumanMethylation27k"" in the file name, Level 1",Batch as the sixth field in the patient barcode,Comments
Batch 34,3,0752,
Batch 37,"1, 2","0945, 1104","0945 comes from 1, one sample that is 1104 comes from 2"
Batch 52,2,1104,
Batch 58,4,1205,
Batch 84,no data,,
Batch 119,no data,,
Batch 144,no data,,
Batch 160,no data,,
Batch 166,no data,,
Batch 183,no data,,
{csv} |
...
Correlation
...
of
...
batch
...
with
...
clinical
...
traits
...
Date:
...
December
...
20th,
...
2011
...
Number
...
of
...
batches
...
based
...
on
...
DNA
...
methylation
...
samples
...
(not
...
necessarily
...
available
...
samples):
...
10
...
Correlation
...
of
...
batch
...
with
...
clinical
...
traits
...
(complete
...
table)
...
can
...
be
...
found
...
Cross-tabulation
...
of
...
batch
...
vs
...
center
...
(two=second
...
field
...
in
...
the
...
patient
...
barcode)
...
| Code Block |
|---|
> table(batchID,two)
two
batchID 05 35 38 44 49 50 53 55 64 67 71 73 75 78 80 86 91 93 95 97 99
0945 0 1 0 7 0 0 0 4 4 5 0 0 0 0 0 0 0 0 0 0 0
1104 3 2 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
1205 14 0 6 1 7 0 0 0 0 0 0 7 0 0 0 0 0 0 0 0 0
1551 0 0 3 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
1626 6 1 0 2 0 7 0 1 6 0 0 0 2 0 1 0 0 0 0 0 0
1756 3 0 3 5 1 13 0 1 0 4 0 2 9 0 0 1 0 0 0 0 0
1856 8 0 0 6 9 6 0 2 0 0 1 0 0 0 0 0 5 0 0 0 0
1947 0 0 0 0 1 1 0 16 0 0 0 0 5 0 2 1 5 0 2 0 0
2037 0 0 1 1 0 1 0 6 0 0 0 0 0 17 0 0 0 1 0 5 1
2064 0 0 0 9 0 0 2 1 2 0 0 0 0 11 0 2 0 0 1 0 0{code}
|
Significant
...
correlations
...
of
...
batch
...
with
...
the
...
clinical
...
variables:
...
| Wiki Markup |
|---|
{csv}"LUAD_clinical_traits","DataType","NumberOfNAs","Test","Pvalue"
"distant_metastasis_pathologic_spread","factor",115,"Pearson's Chi-squared test",5.22E-09
"days_to_form_completion","integer",124,"Kruskal-Wallis rank sum test",6.42E-04
"year_of_initial_pathologic_diagnosis","integer",108,"Kruskal-Wallis rank sum test",1.98E-03
"vital_status","factor",108,"Pearson's Chi-squared test",4.50E-03
{csv} |
...
Most
...
likely
...
that
...
days
...
to
...
form
...
completion
...
is
...
not
...
a
...
real
...
clinical
...
trait.
...
DNA methylation data (tumor
...
matched):
...
27k,
...
available
...
32
...
patients.
...
At
...
this
...
point
...
it
...
is
...
not
...
enough
...
to
...
proceed
...
with
...
analyses