|
|
@@ -1159,6 +1159,39 @@ Methods
|
|
|
fRMA
|
|
|
\end_layout
|
|
|
|
|
|
+\begin_layout Standard
|
|
|
+For testing RMA against fRMA, a data set of 157 hgu133plus2 arrays was used,
|
|
|
+ consisting of blood samples from kidney transplant patients whose grafts
|
|
|
+ had been graded as TX, AR, or ADNR via biopsy and histology
|
|
|
+\begin_inset CommandInset citation
|
|
|
+LatexCommand cite
|
|
|
+key "Kurian2014"
|
|
|
+literal "true"
|
|
|
+
|
|
|
+\end_inset
|
|
|
+
|
|
|
+.
|
|
|
+ These were split into a training set (23 TX, 35 AR, 21 ADNR) and a validation
|
|
|
+ set (23 TX, 34 AR, 21 ADNR).
|
|
|
+ Additionally, an external validation was gathered from public GEO data
|
|
|
+ (37 TX, 38 AR, no ADNR).
|
|
|
+\end_layout
|
|
|
+
|
|
|
+\begin_layout Standard
|
|
|
+\begin_inset Flex TODO Note (inline)
|
|
|
+status collapsed
|
|
|
+
|
|
|
+\begin_layout Plain Layout
|
|
|
+Find appropriate GEO identifiers if possible.
|
|
|
+ Kurian 2014 says GSE15296, but this seems to be different data.
|
|
|
+ I also need to look up the GEO accession for the external validation set.
|
|
|
+\end_layout
|
|
|
+
|
|
|
+\end_inset
|
|
|
+
|
|
|
+
|
|
|
+\end_layout
|
|
|
+
|
|
|
\begin_layout Itemize
|
|
|
Expression array normalization for detecting acute rejection
|
|
|
\end_layout
|
|
|
@@ -1262,8 +1295,7 @@ Classifier probabilities on validation samples when normalized with RMA
|
|
|
The initial data set for testing fRMA consisted of 157 hgu133plus2 arrays,
|
|
|
split into a training set (23 TX, 35 AR, 21 ADNR) and a validation set
|
|
|
(23 TX, 34 AR, 21 ADNR), along with an external validation set gathered
|
|
|
- from public GEO data (37 TX, 38 AR, no ADNR), all on standard hgu133plus2
|
|
|
- Affy arrays
|
|
|
+ from public GEO data (37 TX, 38 AR, no ADNR)
|
|
|
\begin_inset CommandInset citation
|
|
|
LatexCommand cite
|
|
|
key "Kurian2014"
|
|
|
@@ -1272,16 +1304,6 @@ literal "true"
|
|
|
\end_inset
|
|
|
|
|
|
.
|
|
|
-
|
|
|
-\begin_inset Flex TODO Note (inline)
|
|
|
-status open
|
|
|
-
|
|
|
-\begin_layout Plain Layout
|
|
|
-Find out if PAX or BX
|
|
|
-\end_layout
|
|
|
-
|
|
|
-\end_inset
|
|
|
-
|
|
|
To demonstrate the problem, we considered the problem of training a classifier
|
|
|
to distinguish TX from AR using the TX and AR samples from the training
|
|
|
set and validation set as training data, evaluating performance on the
|
|
|
@@ -1400,7 +1422,7 @@ Non-standard platform hthgu133pluspm - no pre-built fRMA vectors available,
|
|
|
\begin_inset Float figure
|
|
|
wide false
|
|
|
sideways false
|
|
|
-status open
|
|
|
+status collapsed
|
|
|
|
|
|
\begin_layout Plain Layout
|
|
|
\begin_inset Graphics
|
|
|
@@ -1439,7 +1461,7 @@ Effect of batch size selection on number of batches included in fRMA probe
|
|
|
\begin_inset Float figure
|
|
|
wide false
|
|
|
sideways false
|
|
|
-status open
|
|
|
+status collapsed
|
|
|
|
|
|
\begin_layout Plain Layout
|
|
|
\begin_inset Graphics
|
