ubic.basecode.datafilter

Class RowLevelFilter<R,C>

java.lang.Object

ubic.basecode.datafilter.AbstractFilter<DoubleMatrix<R,C>,R,C,Double>

ubic.basecode.datafilter.AbstractLevelFilter<R,C>

ubic.basecode.datafilter.RowLevelFilter<R,C>

All Implemented Interfaces:

Filter<DoubleMatrix<R,C>,R,C,Double>

public class RowLevelFilter<R,C>
extends AbstractLevelFilter<R,C>

Remove rows from a matrix based on some row-based statistic. Rows with values too high and/or too low can be removed. Thresholds are inclusive (i.e., values must be at least as high as the set threshold to be included. A number of statistics are available. In addition, this filter can remove rows that have all negative data values.

There are a number of decisions/caveats to consider:

Cutpoint determination

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).

Filtering ratiometric data

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 RowNameFilterto select the rows from the ratio data.

Negative values

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.

Behavior at extremes

If you request removal/inclusion of 1.0 of the data, you might not get the result you expect because the filtering is inclusive.

Author:

Paul Pavlidis

Field Summary

Fields

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

Fields inherited from class ubic.basecode.datafilter.AbstractLevelFilter

highCut, lowCut, useHighAsFraction, useLowAsFraction

Fields inherited from class ubic.basecode.datafilter.AbstractFilter

log

Constructor Summary

Constructors

Constructor and Description
RowLevelFilter()

Method Summary

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.

Methods inherited from class ubic.basecode.datafilter.AbstractLevelFilter

setHighCut, setHighCut, setLowCut, setLowCut, setUseAsFraction, setUseHighCutAsFraction, setUseLowCutAsFraction

Methods inherited from class ubic.basecode.datafilter.AbstractFilter

getOutputMatrix

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

CV

public static final int CV

Use the coefficient of variation as the criterion

See Also:

Constant Field Values

MAX

public static final int MAX

Use the maximum of the row as the criterion.

See Also:

Constant Field Values

MEAN

public static final int MEAN

Use the mean as the criterion.

See Also:

Constant Field Values

MEDIAN

public static final int MEDIAN

Use the median as the criterion.

See Also:

Constant Field Values

MIN

public static final int MIN

Use the minimum of the row as the criterion.

See Also:

Constant Field Values

RANGE

public static final int RANGE

Use the range as the criterion

See Also:

Constant Field Values

Constructor Detail

RowLevelFilter

public RowLevelFilter()

Method Detail

filter

public DoubleMatrix<R,C> filter(DoubleMatrix<R,C> data)

Description copied from interface: Filter

Filter the data

Parameters:

data -

Returns:

setMethod

public void setMethod(int method)

Choose the method that will be used for filtering. Default is 'MAX'. Those rows with the lowest values are removed during 'low' filtering.

Parameters:

method - one of the filtering method constants.

setRemoveAllNegative

public void setRemoveAllNegative(boolean t)

Set the filter to remove all rows that have only negative values. This is applied BEFORE applying fraction-based criteria. In other words, if you request filtering 0.5 of the values, and 0.5 have all negative values, you will get 0.25 of the data back. Default = false.

Parameters:

t - boolean