Question: log vs square-root transformation
gravatar for igor
4 weeks ago by
United States
igor7.1k wrote:

Traditionally, people log-transform expression data. I recently saw someone square-root transform their data. Is there a reason that method is not more widely used? One of the clear benefits is that it will work with 0s, so there is no need to add a pseudocount to the entire matrix, which will disproportionally impact the low values.

rna-seq normalization • 196 views
ADD COMMENTlink modified 20 days ago by Biostar ♦♦ 20 • written 4 weeks ago by igor7.1k

I guess log transformation more efficiently takes care of large differences in read counts.

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Adding a tiny pseudocount like 0.1 probably does not really harm any downstream analysis, because low counts will still be low and lack power for differential analysis and high counts will not effectively be changed.

ADD REPLYlink written 4 weeks ago by ATpoint11k

Log transform symmetrizes under-expression and over-expression representations.

ADD REPLYlink written 4 weeks ago by jomo018450


ADD REPLYlink written 4 weeks ago by Santosh Anand4.3k
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