How to do normalization?

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Xianghui Liu

Feb 17, 2021, 5:13:57 AM2/17/21
to NGLess
Dear Luis:
The example scripts you provided used 'scaled'.  However, I am trying to do use 'seqname' and ' raw' to get the count table first and then do the normalisation by myself.  From the help, there are four mode. Could you kindly explain more about the equation you used for these modes?  Or can I do that use another package for the count table?

normalization specifies if and how to normalize to take into account feature size:

·         {raw} (default) is no normalization

·         {normed} is the result of the {raw} mode divided by the size of the feature

·         {scaled} is the result of the {normed} mode scaled up so that the total number of counts is identical to the {raw} (within rounding error)

·         {fpkm} is fragments per 1000 bp per million fragments, so it is normalized by both the size of the feature and the number of fragments.

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