This seems simple maths behind, But I always get confused with the terminology of **"Fold change", "Log Fold Change" *(LFC)*, and  "Percentage of Change"**., When I see some of the figure descriptions given in **volcano plots**, specially X axis, I get confused. 

i.e. [Page 64][1] 

<a href="https://ibb.co/LtmQF2Q"><img src="https://i.ibb.co/zRp8M08/Capture.jpg" alt="Capture" border="0"></a>


When I google, I found [this figure][2] is easy to understand, but the figure description does not make sense for me. 
<a href="https://ibb.co/gFcsTDw"><img src="https://i.ibb.co/vvM2PJm/volcano-plot-chart-static.png" alt="volcano-plot-chart-static" border="0"></a>

for e.g.
If we take two-fold change;
isn't this the way we calculate LFC;

    LFC = Log2 (Foldchange) = Log2(2) =>1

if X axix is in Log2 fold change, shouldn't two-fold change denotes at **± 1**? Why they denote 2 fold change cutoff line in **± 2**?

-----------------
**Below VP; Fold Change greater than 2 times and significant P value less than 0.05**

See this example:

![enter image description here][3]


and this:

![enter image description here][4]

Could someone help me to understand this terminology ( **"Fold change", "Log Fold Change" *(LFC)*, and  "Percentage of Change"**. ) easily with an example? 


  [1]: http://www.nathalievialaneix.eu/doc/pdf/tutorial-rnaseq.pdf
  [2]: https://documentation.partek.com/display/FLOWDOC/Volcano+Plot
  [3]: https://cdn.xlstat.com/uploads/assets/Tutorials/DifferentialExpression/differentialExpression06.png
  [4]: http://chenyuan.date/images/Volcano-plot-unnamed-chunk-4-1.png

All the figures you posted above shows same thing which is Log2(FoldChange). Although 1st figure x axis labeled "Fold Change" it is Log2(FoldChange). Without log you cannot have negative values (It means down regulated genes). 

One of the reasons to use log2(FoldChange) and not FoldChange only is to use same magnitude for UP and DOWN regulated genes. See the example below. 

Let's say you have 2 genes one **GeneA** and **GeneB**. 

**GeneA** has FPKM (or RPKM) value is **100 in control** and **value 200 in treatment**. 
`FoldChange for GeneA is : (treatment/control =  200 / 100 =  2 )`. 

**GeneB** has FPKM (or RPKM) value is **200 in control** and value **100 in treatment**. 
`FoldChange for GeneB is : (treatment/control =  100 / 200 =  1/2)`. 


As you can see from FoldChange values, **GeneA is  2 fold UP** while **GeneB is 1/2  (0.05) fold down**. Comparison of value 2 and 0.05 are less interpretable to indicate UP and DOWN gene regulation. However,   normalising both UP and DOWN on log2 make UP and DOWN comparisons easy. For e.g. Log2FC for GeneA is 1 and GeneB is -1 which makes fold change comparable and so easy to plot figures (volcano , heatmap etc. ).   

In most RNAseq people use 1.5  or 2 foldChange cutoff. It  means  Log2FC  0.6 and 1 respectively.

In short, log2FC value  >= 0.6 & =< -0.6  suggests 1.5 fold cutoff  and  log2FC value  >= 1 & =< -1 suggests 2 fold cutoff. 






 