Difference between revisions of "RescalePseudoLog"
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| − | An example of the usefulness of pseudolog rescaling is presented in the | + | An example of the usefulness of pseudolog rescaling is presented in the View [http://fantom.gsc.riken.jp/zenbu/gLyphs/#config=ATMu21bIIZvgCegdIRpteD;loc=hg19::chr8:124010566..124067231 "pseudolog rescaling example.1 " ], with the wold lab ENCODE RNA-seq displayed as a heatmap and with expression collated and RPKM normalized onto gencodeV10 models and is rescaled as pseudo_log2 and pseudo_log10, providing a good overview of expression pattern dynamics throughout a wide range of expression levels |
| + | [[image:pseudolog_rescaling.1.png|400px]] | ||
Revision as of 15:11, 14 October 2012
Description
The RescalePseudoLog processing module is a simple signal processor 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 1 or 0.5 to all values).
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
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>
An example of the usefulness of pseudolog rescaling is presented in the View "pseudolog rescaling example.1 " , with the wold lab ENCODE RNA-seq displayed as a heatmap and with expression collated and RPKM normalized onto gencodeV10 models and is rescaled as pseudo_log2 and pseudo_log10, providing a good overview of expression pattern dynamics throughout a wide range of expression levels
