Question: Group definition and logFC calculation in GEO2R
0
gravatar for Kim
4 months ago by
Kim0
Kim0 wrote:

Hello everyone

I'm learning to analyze GEO data and using GEO2R is the most straightforward to me, but I'm having problem understanding how GEO2R (or limma) calculate the logFC.

I read this link https://wiki.bits.vib.be/index.php/Analyze_GEO_data_with_GEO2R and noticed this:

"First define the treated group (it will be colored in blue), then define the control group (it will be colored in pink). The order is important for calculating log fold changes later in the analysis"

The result looks like this https://ibb.co/CKdRkSz

It seems to me that logFC is calculated in GEO2R as logFC = log(control/treated) (or log(normal/tumor) in this case) However, I've read from several sources that logFC = log(treated/ control)

This is confusing me in interpreting gene expression level. Could you please help explain this to me.

Thank you very much.

logfc geo2r group definition • 331 views
ADD COMMENTlink modified 4 months ago • written 4 months ago by Kim0
1
gravatar for Kevin Blighe
4 months ago by
Kevin Blighe52k
Kevin Blighe52k wrote:

The logFC (to be proper, it is log [base 2] fold change) calculation can have anything as the numerator and anything as the denominator. It is your role as the analyst to define these.

Consider the example for geneX:

  • Tumour geneX = 16
  • Normal geneX = 4

.

log2FC = log2(Tumour / Normal) = log2(16 / 4) = 2
log2FC = log2(Normal / Tumour) = log2(4 / 16) = -2

See the difference? Now, you choose what you want as the numerator and denominator.

Kevin

ADD COMMENTlink written 4 months ago by Kevin Blighe52k

Hi Kevin

Thank you for your comment. I agree that what we choose as numerator and denominator are up to our decision. I'm just confused as GEO2R always take Pink/ Blue (control/ treatment) while some people say it's always treatment/ control. But it's useful to know there's no fixed rule on log2FC calculation.

ADD REPLYlink written 4 months ago by Kim0

I believe you can change the order via GEO2R, but I do not use it too much.

ADD REPLYlink written 4 months ago by Kevin Blighe52k
0
gravatar for Kim
4 months ago by
Kim0
Kim0 wrote:

I also emailed GEO2R team and they've just replied. For anyone who has the same question:

"The first group that is named in the 'Define groups' drop-down menu becomes the denominator in logFC, and the second group that is named becomes the numerator. The background pink/blue colors are not important.

Reversing the order in which you name groups will result in a reversed sign in logFC (e.g., 4 vs. -4)."

ADD COMMENTlink written 4 months ago by Kim0
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