Question: log vs square-root transformation
2
gravatar for igor
3 months ago by
igor7.3k
United States
igor7.3k 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 • 335 views
ADD COMMENTlink modified 11 weeks ago by Biostar ♦♦ 20 • written 3 months ago by igor7.3k
2

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

enter image description here

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 3 months ago by ATpoint13k
1

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

ADD REPLYlink written 3 months ago by jomo018470
1

see https://stats.stackexchange.com/a/107690

ADD REPLYlink written 3 months ago by Santosh Anand4.6k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1284 users visited in the last hour