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nia
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@nia-12707
Last seen 4.0 years ago

Hi everyone,
I have write a script to analyze microarray illumina data by using Limma package. The script generated a table and it consist a logFC column. Now, I wish to know the FC values but here I have a confusion that should I go with `2^logFC`

or `10^logFC`

. I am looking for help.

Thankyou for the quick response, that means I have to go with

`2^logFC`

.Yes.

Alternatively, you can use

`sign(logFC)*2^abs(logFC)`

which has some symmetrical properties.For a logFC of

`-3`

, instead of getting`2^-3 = 1/8 = 0.125`

, you get`-8`

.Here you have to interpret

`-x`

as`1/x`

. This could help. Of course, there is no in`]-1:1[`

.Very detailed information thank you. The point I learn is if I do

`2^logFC`

then I have to interpret that -logfc as 1/-logfc.No I understand what you mean. Here is what I mean:

If logFC = 3, then FC = 2^3 = 8

If logFC = -3, then FC = 2^-3 = 1/8 that can also be noted -8 using the convention that -x means 1/x

I can't help but feel that this notation causes more problems than it solves; having the magnitude of the fold-change and the sign of the log-fold change is begging to be mistaken for one or the other. Certainly, if I saw a negative "fold change" in an analysis report, I would assume that the author made a typo and actually meant "log-fold change".

If one finds log-values or fold-changes below 1 too difficult to comprehend, a more mathematically appropriate notation would be to state

`1/x`

rather than`-x`

, where`x = 2^abs(logFC)`

for`logFC < 0`

. Then you get the magnitude of the fold change without repurposing the minus symbol to represent something other than its intended meaning.