Question: Difference between FC and LogFC
7
gravatar for Joe Kherery
2.7 years ago by
Joe Kherery110
Joe Kherery110 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 • 16k views
ADD COMMENTlink modified 2.7 years ago by Alex Reynolds31k • written 2.7 years ago by Joe Kherery110
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 2.7 years ago by WouterDeCoster45k
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 2.7 years ago by h.mon32k

Ty so much WouterDeCoster

ADD REPLYlink written 2.7 years ago by Joe Kherery110
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 2.7 years ago • written 2.7 years ago by h.mon32k

Thank you so much h.mon, Useful links.

ADD REPLYlink written 2.7 years ago by Joe Kherery110
1

fold chance

Do you mean fold change?

ADD REPLYlink written 2.7 years ago by _r_am32k

Hello Ram, sorry!

Yes, Fold change (FC)

ADD REPLYlink written 2.7 years ago by Joe Kherery110
8
gravatar for Russ
2.7 years ago by
Russ470
Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
Russ470 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 2.7 years ago by Russ470
6
gravatar for russhh
2.7 years ago by
russhh5.5k
UK, U. Glasgow
russhh5.5k 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 2.7 years ago by russhh5.5k

Thank you so much russhh,

ADD REPLYlink written 2.7 years ago by Joe Kherery110
4
gravatar for Alex Reynolds
2.7 years ago by
Alex Reynolds31k
Seattle, WA USA
Alex Reynolds31k 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 2.7 years ago • written 2.7 years ago by Alex Reynolds31k
2
gravatar for Jeremy Leipzig
2.7 years ago by
Philadelphia, PA
Jeremy Leipzig19k 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 2.7 years ago by Jeremy Leipzig19k
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: 2319 users visited in the last hour
_