Question: Difference between FC and LogFC
4
gravatar for Joe Kherery
14 months ago by
Joe Kherery60
Joe Kherery60 wrote:

Hello guys,

It may seem like a basic question, but this is causing confusion.

What is the difference between fold change and Log fold change?

Regards,

microarray R • 5.4k views
ADD COMMENTlink modified 14 months ago by Alex Reynolds28k • written 14 months ago by Joe Kherery60
7

Using a log has some advantages here. Without the log, a downregulation gets squeezed between 0 and 1, while an upregulation goes from 1 to infinity. With the log, you get a better scale.

ADD REPLYlink written 14 months ago by WouterDeCoster40k
2

With the log, you get a better scale.

Indeed, centered around zero and symmetrical, instead of centered around one and asymmetrical.

ADD REPLYlink written 14 months ago by h.mon26k

Ty so much WouterDeCoster

ADD REPLYlink written 14 months ago by Joe Kherery60
2

Log fold change = log(FC)

Usually, the transformation is log at base 2, so the interpretation is straightforward: a log(FC) of 1 means twice as expressed.

See some lengthier discussions here and here.

ADD REPLYlink modified 14 months ago • written 14 months ago by h.mon26k

Thank you so much h.mon, Useful links.

ADD REPLYlink written 14 months ago by Joe Kherery60
1

fold chance

Do you mean fold change?

ADD REPLYlink written 14 months ago by RamRS23k

Hello Ram, sorry!

Yes, Fold change (FC)

ADD REPLYlink written 14 months ago by Joe Kherery60
7
gravatar for Russ
14 months ago by
Russ450
Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
Russ450 wrote:

I find pictures helpful when thinking about these concepts, so quickly made some visualizations for you. They expand on WouterDeCoster's and h.mon's comments. The figures were made in R using with the following code:

#Generate fake data    
fake <- data.frame("gene" = as.numeric(c(1:50)), "pre" = as.numeric(seq(1,99,2)), "post"= as.numeric(seq(99,1,-2)))
#Calculate fold change
fake$fold <- fake$post/fake$pre
#Calculate log2 fold change
fake$logfold <- log2(fake$fold)
#Visualize
library(ggplot2)
ggplot(fake, aes(x = gene, y = fold)) + geom_line()
ggplot(fake, aes(x = gene, y = logfold)) + geom_line() + ylab("Log2(FC)")

Let's say you have 50 genes (for the sake of convenience, the genes are called "1", "2", "3", ... , "50") and you measure expression before and after some type of treatment. You then measure the fold change of the genes due to treatment: FC = expression(post) / expression(pre). As russhh indicated, the logFC is simply log2(FC).

In this dataset, half the genes were upregulated and the other half downregulated. Interpreting the untransformed fold change is tricky: here it looks like gene1 had a huge fold change, close to 100, but what about genes30-50? It's hard to tell what their value is, and also by how much they differ from each other.

enter image description here

Performing the log2 transformation scales the data and facilitates the interpretation, as illustrated below.

enter image description here

The differences in expression in genes30-50 are now much more obvious.

ADD COMMENTlink written 14 months ago by Russ450
6
gravatar for russhh
14 months ago by
russhh4.6k
UK, U. Glasgow
russhh4.6k wrote:

If you think that fold-change is the 'expression level' in one set of samples (set A) divided by the 'expression level' in another set (set B), then log-fold-change is the log of that value (typically to base 2).

That is, if FC=, A/B, then log_FC = log(A / B) = log(A) - log(B)

and if log_FC=x, then FC=2^x

ADD COMMENTlink written 14 months ago by russhh4.6k

Thank you so much russhh,

ADD REPLYlink written 14 months ago by Joe Kherery60
4
gravatar for Alex Reynolds
14 months ago by
Alex Reynolds28k
Seattle, WA USA
Alex Reynolds28k wrote:

To follow up on the value added by the symmetry in log2-transformed fold changes, you might also look at a volcano plot of features, a common way to represent p-values vs log2-fold change.

For example:

enter image description here

Symmetry makes visual interpretation of this type of plot — comparison and labeling of features with significant fold change and p-value thresholds — much simpler. One can see immediately which features are both statistically significant and likely to be significantly up- or down-regulated.

ADD COMMENTlink modified 14 months ago • written 14 months ago by Alex Reynolds28k
2
gravatar for Jeremy Leipzig
14 months ago by
Philadelphia, PA
Jeremy Leipzig18k wrote:

"fold change" is a bad metric and also the term itself can be ambiguous when speaking to different people, as evidenced by the confused entry in wikipedia https://en.wikipedia.org/wiki/Fold_change

"log2 fold change" is symmetric and unambiguous

ADD COMMENTlink written 14 months ago by Jeremy Leipzig18k
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