Question: % of change and log2 fold change (L2FC)?
2
gravatar for Wox
11 months ago by
Wox310
HUJI
Wox310 wrote:

I am trying to understand Gene expression data analysis. Could someone the percentage of change of the GE calculating from log2 fold change (L2FC)?

FoldChange = μ_Treatment / μ_Control

log2FC=Log2(μ_Treatment)-Log2(μ_Control)

rna-seq gene • 811 views
ADD COMMENTlink modified 11 months ago • written 11 months ago by Wox310
5
gravatar for geek_y
11 months ago by
geek_y10k
Barcelona
geek_y10k wrote:

seems correct to me. log2FC is more informative as you will see the direction (sign) and the effect.

Treatment = 10
Control = 100

FoldChange = 10/100 = 0.1 which is not informative

log2FC = log2(10)-log2(100) = -3.3 which tells the effect and direction.

ADD COMMENTlink modified 11 months ago • written 11 months ago by geek_y10k

Thank you @geek_y.

After getting log2FC; e.g. -3.3, how can we calculate the % of change? is that %change = (Change/Original) x 100 ?

ADD REPLYlink written 11 months ago by Wox310
2

If you do 2^log2FC, which tells how many folds the change is. Here 2^3.3=9.8 folds. The sign gives information about the up/down regulation.

ADD REPLYlink modified 11 months ago • written 11 months ago by geek_y10k
2
gravatar for Wox
11 months ago by
Wox310
HUJI
Wox310 wrote:

calculate fold change (FC) When comparing these log transformed values, we use the quotient rule of logarithms:

log(A/B) = log(A) - log(B)

log(A) = 4

log(B) = 1

Therefore:

log(A/B) = 4 - 1

log(A/B) = 3 This gives a 3-fold change.

Please note that in this case we are reporting the log(fold change). Biologists often use the log(fold change) because without taking the log, down regulated genes would have values between 0 and 1, whereas up regulated genes would have any value between 1 and infinity. This distribution makes graphing and further statistical analysis difficult. Taking the log typically makes the resulting values more normally distributed, which is better for further analysis.

ADD COMMENTlink modified 11 months ago • written 11 months ago by Wox310
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