# Difference between revisions of "RescalePseudoLog"

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− | The '''RescalePseudoLog''' [[DataProcessing#Processing_modules|processing module]] is a simple signal procesor which rescale expression level as pseudo log. | + | The '''RescalePseudoLog''' [[DataProcessing#Processing_modules|processing module]] is a simple signal procesor which rescale expression level as pseudo log.<br> |

Log transformation is convenient to vizualize data whose expression levels varies in a wide range of values, but zero values are common places and log(base,0) is not defined and we would thus need to recurse to pseudocount (typically arbitrarily adding 0.5). | Log transformation is convenient to vizualize data whose expression levels varies in a wide range of values, but zero values are common places and log(base,0) is not defined and we would thus need to recurse to pseudocount (typically arbitrarily adding 0.5). | ||

## Revision as of 20:41, 21 May 2012

## Description

The **RescalePseudoLog** processing module is a simple signal procesor which rescale expression level as pseudo log.

Log transformation is convenient to vizualize data whose expression levels varies in a wide range of values, but zero values are common places and log(base,0) is not defined and we would thus need to recurse to pseudocount (typically arbitrarily adding 0.5).

Alternatively we can use pseudolog defined as **asinh(x/2) / log(base)**, which
has the following nice properties

- is defined for all real x values
- pseudolog(base, 0) = 0
- pseudolog(base, -x) = -1* pseudolog(base, x)
- pseudolog(base, x) ~ log(base, x) for x > base values

For information : pseudolog(10,1) = 0.2089876; log10(1) = 0 pseudolog(10,2) = 0.3827757; log10(2) = 0.3010300 pseudolog(10,3) = 0.5188791; log10(3) = 0.4771213 pseudolog(10,4) = 0.6269629; log10(4) = 0.6020600 pseudolog(10,5) = 0.7153834; log10(5) = 0.6989700 pseudolog(10,10) = 1.0042792; log10(10) = 1 pseudolog(10,100)= 2.0000430; log10(100)= 2 pseudolog(2,1) = 0.6942419; log2(1) = 0 pseudolog(2,2) = 1.2715533; log2(2) = 1 pseudolog(2,3) = 1.7236790; log2(3) = 1.584963 pseudolog(2,4) = 2.0827257; log2(4) = 2 pseudolog(2,5) = 2.3764522; log2(5) = 2.321928 pseudolog(2,10) = 3.3361433; log2(10) = 3.321928 pseudolog(2,100)= 6.6440004; log2(100)= 6.643856

## Parameters

The sole optional parameter is the base of the pseudo log rescaling. By default, the rescaling base is set to 10

## Example

Simple script...

<zenbu_script> <stream_queue> <spstream module="RescalePseudoLog"> <base>10</base> </spstream> </stream_queue> </zenbu_script>