| Bioinformatics Toolbox | |
Remove gene profiles with low absolute values
Mask = genelowvalfilter(Data,
'PropertyName', PropertyValue...)
[Mask, FData] = genelowvalfilter(Data)
[Mask, FData, FNames] = genelowvalfilter(Data, Names)
genelowvalfilter(..., 'Prctile', PrctileValue)
genelowvalfilter(..., 'AbsValue', AbsValueValue)
genelowvalfilter(..., 'AnyVal', AnyValValue)
Data | 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. |
Prctile | Property to specify a percentile below which gene expression profiles are removed. Enter a value from 0 to 100. |
| AbsValue | Property to specify an absolute value below which gene expression profiles are removed. |
| AnyVal | Property to select the minimum or maximum absolute value for comparison with AbsValue. If AnyValValue is true, selects the minimum absolute value. If AnyVal is false, selects the maximum absolute value. The default value is false. |
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, 'PropertyName', PropertyValue...) 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 a filtered data matrix (FData). FData can also be created using FData = Data(find(I),:).
[Mask, FData,FNames] = genelowvalfilter(Data, Names) returns a filtered names array (FNames), where Names is a cell array of the names of the genes corresponding to each row of Data. FNames can also be created using FNames = Names(I).
genelowvalfilter(..., 'Prctile', PrctileValue) removes from Data gene expression profiles with all absolute values less than the percentile Prctile.
genelowvalfilter(..., 'AbsValue', AbsValueValue) calculates the maximum absolute value for each gene expression profile and removes the profiles with maximum absolute values less than AbsVal.
genelowvalfilter(..., 'AnyVal', AnyValValue), when AnyVal is true, calculates the minimum absolute value for each gene expression profile and removes the profiles with minimum absolute values less than AnyVal.
[data, labels, I, FI] = genelowvalfilter(data,labels,'AbsValue',5);
Bioinformatics Toolbox functions exprprofrange, exprprofvar, geneentropyfilter, generangefilter
| | geneentropyfilter | generangefilter | |
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