Values EXCEEDS the original data range after batch effect correction.
Hi
I have gene coverage (%) data in a matrix structure. since the coverage estimated is in percentage, it falls in range of 0-100%. now I ran limma to remove batch effect, and see that the range of gene coverage is now 0-6000
How could it be possible?
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Does limma recommend you use percentages? How is a batch correction algorithm supposed to know the semantic limitations of your metric?
but limma takes normalized values, right? So my coverage was estimated in percentages, which states that it is a normalised value. That's why I used that as an input to limma
the usage for
removeBatchEffectsstates that the input matrix should be aUsing percentages is not consistent with this expectation.
yes, as suggested https://support.bioconductor.org/p/9140296/#9156132 in this post, percentage values are explained how to deal with. However, my output values are in a range that I am NOT confident about. if u could just go through this, https://support.bioconductor.org/p/9140296/#9156132
Thanks