# Re: [galaxy-user] Help!!! cuffdiff log2 value

```Hi Noa,
This is it exactly - thanks for adding in the interpretation!
Jen```
```
On 5/10/12 11:54 AM, Noa Sher wrote:
```
```  I think the sign is to show if it is x-fold more than the first
condition (+) or x-fold less than the first condition (-). A regular
fold would give you values from 1-whatever if sample 2 is more than
sample 1, and a fraction (0-1) if sample 1 is expressed more than sample
2. The log lets you get both on the same scale, so that 2 means (on log2
scale) four-fold upregulated, and -2 means four-fold downregulated.

FPKM x  FPKM y  y/x     log(y/x)
1       2       2       1
1       0.5     0.5     -1

On 10/05/2012 19:00, Jennifer Jackson wrote:
```
```Hi Jiwen,

As far as I know, this is possible. The CuffDiff log2 value is defined

7   FPKMx              8.01089   FPKM of the gene in sample x
8   FPKMy              8.551545     FPKM of the gene in sample y
9   log2(FPKMy/FPKMx)  0.06531     The (base 2) log of the fold
change y/x

And log(2) in general (including a graph, which can help with
visualizing) is described here (although the web is full if similar):
http://en.wikipedia.org/wiki/Logarithm

I can see that this same Q on seqanswers.com recieved pretty much the
are safe using the data as it as generated. Taking a look at the
inputs would be advised if the results were unexpected.

If you do still have concerns about the log(2) calculation, asking the
tool authors directly (if you have't done so already) at
tophat.cuffli...@gmail.com is always an option, to tripple check.

Best,

Jen
Galaxy team

On 4/26/12 7:48 AM, 杨继文 wrote:
```
```Hi,
I am analyzing my RNA-Seq data. After running cuffdiff, I got a list of
differentially expressed transcrpts or genes.
As far as I know, log2 value = fold change. However, there are minus
values. Is this possible?? log2 value can not be minus. Did I miss
something??
Best
Jiwen

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```
```
```

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```
--
Jennifer Jackson
http://galaxyproject.org
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