RescalePseudoLog
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 in genomic data and log(base,0) is not defined.
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>
