Question: How to calculate "fold changes" in gene expression?
7
gravatar for juan.rosas1
3.6 years ago by
juan.rosas170
Puerto Rico
juan.rosas170 wrote:

Hellow I have a question on how to calculate fold changes when analyzing gene expression changes between multiple tumor and control samples per gene?

R gene • 85k views
ADD COMMENTlink modified 2.3 years ago by Vasei20 • written 3.6 years ago by juan.rosas170
6

Let's say there are 50 read counts in control and 100 read counts in treatment for gene A. This means gene A is expressing twice in treatment as compared to control (100 divided by 50 =2) or fold change is 2. This works well for over expressed genes as the number directly corresponds to how many times a gene is overexpressed. But when it is other way round (i.e, treatment 50, control 100), the value of fold change will be 0.5 (all underexpressed genes will have values between 0 to 1, while overexpressed genes will have values from 1 to infinity). To make this leveled, we use log2 for expressing the fold change. I.e, log2 of 2 is 1 and log2 of 0.5 is -1.

Hope this helps

ADD REPLYlink written 3.6 years ago by arnstrm1.7k

@arnstrm what will happen if you have the same number of replicate for both control and treated ? how do you calculate the fold change?

ADD REPLYlink written 2.3 years ago by Learner 110
3
gravatar for Antonio R. Franco
3.6 years ago by
Spain. Universidad de Córdoba
Antonio R. Franco3.9k wrote:

Or the bioconductor limma package if you are dealing with arrays and/or RNA-Seq to analyze your data

Limma will give you the log2 expression changes based upon statistical values

ADD COMMENTlink written 3.6 years ago by Antonio R. Franco3.9k

But how can I use it?

ADD REPLYlink written 2.8 years ago by diana_masa0

Have you read the user's guide?

ADD REPLYlink written 2.8 years ago by Devon Ryan86k
1
gravatar for Ido Tamir
3.6 years ago by
Ido Tamir4.9k
Austria
Ido Tamir4.9k wrote:

You could reinvent the wheel of course, but If you ask such a question, use what pros have put a lot of thought in:

http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html

http://www.bioconductor.org/packages/release/bioc/html/edgeR.html

 

ADD COMMENTlink written 3.6 years ago by Ido Tamir4.9k
4

It should also be noted that if someone has to ask how to do this sort of thing then he/she probably shouldn't be reinventing this particular wheel...

ADD REPLYlink written 3.6 years ago by Devon Ryan86k
0
gravatar for Vasei
2.3 years ago by
Vasei20
Vasei20 wrote:

Fold change can also be computed in unsupervised fashion, where we don't know the class labels(like case-control or type1-type2) of the samples. In that setting we can use mean expression of a gene as the base value and compute the fold change for that gene in each sample.

ADD COMMENTlink written 2.3 years ago by Vasei20

Can you direct to any references or studies used this method. thanks

ADD REPLYlink written 22 months ago by Shyam120
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