Question: Wgcna -Dilemma In Choosing Soft Threshold
gravatar for pixie@bioinfo
7.4 years ago by
Université Paris, Saclay
pixie@bioinfo1.4k wrote:

I have two expression matrices (normalized, using dChip), with the same data except that in one of them , the expression values are log-transformed. I am trying to perform WGCNA analysis on them and getting different plots for scale independence.

First image: For the log-transformed values, some of the power-values (like 9,10) seems to approach 0.9 (red line corresponds to 0.9).

Second image: For the plot in which the data is not log-transformed, none of the power-values are falling beyond R^2>=0.9, (the red line corresponds to 0.8). I am in a dilemma as to which beta threshold I should consider and whether one should take log-transformed values or not for the analysis



R • 4.2k views
ADD COMMENTlink modified 7.4 years ago • written 7.4 years ago by pixie@bioinfo1.4k

In general, for microarray expression, you will want to log-transform the data before proceeding. A lot of methodologies make implicit assumptions of "normality" that will hold approximately for log-transformed data but will not for linear-scale expression values.

ADD REPLYlink written 7.4 years ago by Sean Davis26k

thank you so much for the insight..i was really confused regarding this

ADD REPLYlink written 7.4 years ago by pixie@bioinfo1.4k

Which log transform should we apply? log2? 



ADD REPLYlink written 5.6 years ago by madkitty620
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