Question: what does a log 2-fold change values of mean ?
1
gravatar for a4appy23
7 months ago by
a4appy2310
a4appy2310 wrote:

Im new to bioinformatics and trying to figure out log 2 FC..

i have a log 2 fold values of a parts of a gene in full sequence which is listed below using micro arrays. log2-fold change -0.611040 -0.583231 -0.495397 -0.462919 0.412907 0.405912 which goes on

does negative value mean down regulation and positive valuse mean up regulation ?? like the values with 0 ,1 or -1

ADD COMMENTlink modified 7 months ago • written 7 months ago by a4appy2310
5
gravatar for lieven.sterck
7 months ago by
lieven.sterck5.2k
VIB, Ghent, Belgium
lieven.sterck5.2k wrote:

From wikipedia:

In the field of genomics (and more generally in bioinformatics), the modern usage is to define fold change in terms of ratios, and not by the alternative definition.[9][10] However, log-ratios are often used for analysis and visualization of fold changes. The logarithm to base 2 is most commonly used,[9][10] as it is easy to interpret, e.g. a doubling in the original scaling is equal to a log2 fold change of 1, a quadrupling is equal to a log2 fold change of 2 and so on. Conversely, the measure is symmetric when the change decreases by an equivalent amount e.g. a halving is equal to a log2 fold change of −1, a quartering is equal to a log2 fold change of −2 and so on.

and eg other posts here on Biostars: Understanding up and down regulated genes from LOG2 foldchange or foldchange

in other words: have you tried googling it first?

ADD COMMENTlink modified 7 months ago • written 7 months ago by lieven.sterck5.2k

yes i did...i was trying to find out what does positive and negative value of log2FC mean.

ADD REPLYlink written 7 months ago by a4appy2310
3

Imagine you are calculating fold-change by measuring counts ratios, so:

FoldChange = counts( Treatment ) / Counts ( Control )

Here, FoldChange values larger than one means the gene is more expressed in Treatment, a FoldChange of exactly one means no difference, and FoldChange values between zero and one means the gene is more expressed in Control. Now, if you take the log base 2 of the FoldChange values, you will have:

  • if FoldChange > 1, log2( FoldChange ) > 0
  • if FoldChange = 1, log2( FoldChange ) = 0
  • if 0 < FoldChange < 1, log2( FoldChange ) < 0

So positive values means the gene is more expressed in Treatment, and negative values means the gene is more expressed in Control.

ADD REPLYlink written 7 months ago by h.mon25k

thank you for the reply...it really helped..

ADD REPLYlink written 7 months ago by a4appy2310
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