public class RowLevelFilter<R,C> extends AbstractLevelFilter<R,C>
There are a number of decisions/caveats to consider:
There are multiple ways of determining cutpoints. Some possibilities are the maximum value, the minimum value, the mean value, or the median value. The range and coefficient of variation are also included.
Note that if you want to use different methods for high-level filtering than for low-level filtering (e.g., using max for the low-level, and min for the high-level, you have to filter twice. This could cause problems if you are using fractional filtering and there are negative values (see below).
For data that are normalized or ratios, it does not make sense to use this method on the raw data. In that situation,
you should filter the data based on the raw data, and then use a RowNameFilter
to select the rows from the
ratio data.
For microarray expression data based on the Affymetrix MAS4.0 protocol (and possibly others), negative values can occur. In some cases all the values can be negative. As these values are generally viewed as nonsensical, one might decide that data rows that are all negative should be filtered.
If you request removal/inclusion of 1.0 of the data, you might not get the result you expect because the filtering is inclusive.
Modifier and Type | Field and Description |
---|---|
static int |
CV
Use the coefficient of variation as the criterion
|
static int |
MAX
Use the maximum of the row as the criterion.
|
static int |
MEAN
Use the mean as the criterion.
|
static int |
MEDIAN
Use the median as the criterion.
|
static int |
MIN
Use the minimum of the row as the criterion.
|
static int |
RANGE
Use the range as the criterion
|
highCut, lowCut, useHighAsFraction, useLowAsFraction
log
Constructor and Description |
---|
RowLevelFilter() |
Modifier and Type | Method and Description |
---|---|
DoubleMatrix<R,C> |
filter(DoubleMatrix<R,C> data)
Filter the data
|
void |
setMethod(int method)
Choose the method that will be used for filtering.
|
void |
setRemoveAllNegative(boolean t)
Set the filter to remove all rows that have only negative values.
|
setHighCut, setHighCut, setLowCut, setLowCut, setUseAsFraction, setUseHighCutAsFraction, setUseLowCutAsFraction
getOutputMatrix
public static final int CV
public static final int MAX
public static final int MEAN
public static final int MEDIAN
public static final int MIN
public static final int RANGE
public DoubleMatrix<R,C> filter(DoubleMatrix<R,C> data)
Filter
data
- public void setMethod(int method)
method
- one of the filtering method constants.public void setRemoveAllNegative(boolean t)
t
- booleanCopyright © 2003–2023 UBC Michael Smith Laboratories. All rights reserved.