Question: % of change and log2 fold change (L2FC)?
2
gravatar for Wuschel
5 weeks ago by
Wuschel120
HUJI
Wuschel120 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 • 247 views
ADD COMMENTlink modified 5 weeks ago • written 5 weeks ago by Wuschel120
5
gravatar for geek_y
5 weeks ago by
geek_y9.4k
Barcelona/CRG/London/Imperial
geek_y9.4k 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 5 weeks ago • written 5 weeks ago by geek_y9.4k

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 5 weeks ago by Wuschel120
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 5 weeks ago • written 5 weeks ago by geek_y9.4k
2
gravatar for Wuschel
5 weeks ago by
Wuschel120
HUJI
Wuschel120 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 5 weeks ago • written 5 weeks ago by Wuschel120
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