Bioinformatics Toolbox™

genelowvalfilter - Remove gene profiles with low absolute values

Syntax

Mask = genelowvalfilter(Data) [Mask, FData] = genelowvalfilter(Data) [Mask, FData, FNames] = genelowvalfilter(Data, Names) genelowvalfilter(..., 'Percentile', PercentileValue, ...) genelowvalfilter(..., 'AbsValue', AbsValueValue, ...) genelowvalfilter(..., 'AnyVal', AnyValValue, ...)

Arguments

`Data`	`DataMatrix object` or numeric matrix where each row corresponds to the experimental results for one gene. Each column is the results for all genes from one experiment.
`Names`	Cell array with the same number of rows as `Data`. Each row contains the name or ID of the gene in the data set.
`PercentileValue`	Property to specify a percentile below which gene expression profiles are removed. Enter a value from `0` to `100`.
`AbsValueValue`	Property to specify an absolute value below which gene expression profiles are removed.
`AnyValValue`	Property to select the minimum or maximum absolute value for comparison with `AbsValueValue`. If `AnyValValue` is `true`, selects the minimum absolute value. If `AnyValValue` is `false`, selects the maximum absolute value. The default value is `false`.

Description

Gene expression profile experiments have data where the absolute values are very low. The quality of this type of data is often bad due to large quantization errors or simply poor spot hybridization.

Mask = genelowvalfilter(Data) identifies gene expression profiles in Data with all absolute values less than the 10th percentile.

Mask is a logical vector with one element for each row in Data. The elements of Mask corresponding to rows with absolute expression levels greater than the threshold have a value of 1, and those with absolute expression levels less then the threshold are 0.

[Mask, FData] = genelowvalfilter(Data) returns FData, a filtered data matrix. You can also create FData using FData = Data(Mask,:).

[Mask, FData, FNames] = genelowvalfilter(Data, Names) returns FNames, a filtered names array, where Names is a cell array of the names of the genes corresponding to each row of Data. You can also create FNames using FNames = Names(Mask).

Note If Data is a DataMatrix object with specified row names, you do not need to provide the second input Names to return the third output FNames.

genelowvalfilter(..., 'PropertyName', PropertyValue, ...) calls genelowvalfilter with optional properties that use property name/property value pairs. You can specify one or more properties in any order. Each PropertyName must be enclosed in single quotation marks and is case insensitive. These property name/property value pairs are as follows:

genelowvalfilter(..., 'Percentile', PercentileValue, ...) removes from Data, the experimental data, the gene expression profiles with all absolute values less than PercentileValue, the specified percentile.

genelowvalfilter(..., 'AbsValue', AbsValueValue, ...) calculates the maximum absolute value for each gene expression profile and removes the profiles with maximum absolute values less than AbsValValue.

genelowvalfilter(..., 'AnyVal', AnyValValue, ...), when AnyValValue is true, calculates the minimum absolute value for each gene expression profile and removes the profiles with minimum absolute values less than AnyValValue.

Examples

[data, labels, I, FI] = genelowvalfilter(data,labels,'AbsValue',5);

References