Filter List

Predefined filters :
The filters in this list have been built into ArrayMiner for direct use. They may be combined into user-defined filters.

	Logarithm		Replace NAs
	Value to NAs		Low-Pass
	High pass		Low-Pass reject
	High-Pass reject		Add value
	Multiply value		Reject NAs
	Absolut Fold		Relative Fold
	Average to 0		Norm 1
	Sign checker		Restore data
	Gene List Matcher		Gene list rejecter
	Text Matcher		Text Rejecter

Logarithm

This filter applies a natural logarithm transformation to all values of the dataset. If the source value is less or equal to 0, the value is replaced by a missing value field. If all values are missing for a gene, the gene is rejected. The logarithm filter should be applied if your dataset is based on ratia. In this case all your original data should be greater than 0.
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Replace NAs

This filter replaces all missing values by the specified one.

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Value to NAs

This filter replaces all occurences of a specified value by missing values.

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Low-Pass

This filter replaces any value inferior to the specified one, by a specified value.

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High pass

This filter replaces any value greater then the specified one, by a specified value.

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Low-Pass reject

This filter rejects any gene with a value inferior to the specified one.

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High-Pass reject

This filter rejects any gene with a value greater than the specified one.

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Add value

This filter adds a specified value to all non-missing values in the whole dataset (all values in the dataset are increased by the specified amount).

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Multiply value

This filter multiplies all non-missing values by the specified one, in the whole dataset (all values in the dataset are multiplied by the specified value).

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Reject NAs

This filter rejects genes with more missing values than the specified count.

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Absolute Fold

This filter rejects genes that have a smaller Absolute fold than the specified one.

Absolute fold=abs((max value of the gene)-(min value of the gene))
Note : abs(x) is the absolute value of x.
Example : abs(3)=3 abs(-3)=3

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Relative Fold

    This filter reject genes that have a smaller Relative fold than the specified one. If the signs of the maximum and minimum value of a gene are not the same, nothing is done (the gene passes the filter unchanged).

If max and min >0
    Relative fold=(max value of the gene)/(min value of the gene)
Else
    Relative fold=(min value of the gene)/(max value of the gene)

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Average to 0

This filter normalizes all genes toward a 0 average.(Learn more)

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Norm 1

This filter normalizes all genes toward a 1 norm. (Unit normalization Learn more)

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Sign checker

This filter rejects genes that have fewer sign changes than the specified value. In the figure on the right, the red gene has one sign change and the green has three.
Note that if you average your data to 0 and choose a value of 2 for this filter, you will eliminate from the dataset all monotonic profiles, i.e. profiles that are either always increasing (like the red gene on the right) or decreasing.

Restore data

This filter replaces the current values in a profile by those in the original data. This is useful for restoring the data after a complex filtering. For example, if you apply the sign checker example above to reject monotonic genes, adding this filter after the sign checker will eliminate the average-to-0 effect.

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Gene List Matcher

This filter rejects genes that are not included in a specified list. Note that saving a user filter with this filter in the user filter table will also save the specified gene list allowing you to reuse it each time you need it.

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Gene list rejecter

This filter rejects genes that are included in a specified list (this is the inverse of the Gene List Matcher above). Note that saving a user filter containing this filter will also save the specified gene list, allowing you to reuse it each time you need it.

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Text Matcher

This filter rejects genes that do not include a specified pattern in their description field. Note that the string pattern is case sensitive.

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Text Rejecter

This filter rejects genes that do include a specified pattern in their description field. Note that the string pattern is case sensitive.

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