Question: Differences between lfc=log2(1.5) and lcf=1.5
2
gravatar for Joe Kherery
2.1 years ago by
Joe Kherery90
Joe Kherery90 wrote:

Dears,

What is the difference between lfc=log2(1.5) and lcf=1.5 ?

topTable <- topTable(fit, coef=1, number=Inf, adjust.method="BH", **lfc=1.5**)

Which is the correct one to use and why?

Another question is what cut-off to use???

I see many articles using |log2fold change (FC)|≥1.5 and others using |log2fold change (FC)|≥1.0? with a Q-value < 0.05.

If you can tell me a reference about it, I will be grateful

Regards,

microarray limma R • 1.5k views
ADD COMMENTlink modified 2.1 years ago by h.mon29k • written 2.1 years ago by Joe Kherery90
4
gravatar for h.mon
2.1 years ago by
h.mon29k
Brazil
h.mon29k wrote:

What is the difference between lfc=log2(1.5) and lcf=1.5 ?

If you are asking about which one to use in topTable, the correct is topTable( ..., lfc = 1.5 ), as the fold-changes reported (and used for thresholding) are already log2(FC). However, topTable should not be used, and topTreat is to be preferred - read the topTreat manual page with ?topTreat.

As for "correct" threshold, my view is that there isn't one. It is of course necessary to control for false-positive discovery, hence the q-value of 0.05 (or lower). But for fold-changes, I guess it depends on if one is interested in all changes, or only big changes in expression.

One of the benefits of using log2(FC) is that the values are intuitive: a log2(FC) of one means one treatment has double the expression of the other; a log2(FC) of 2 means one treatment is 4 times more expressed than the other, and so on. However, using log2(FC) = 1.5 means one treatment is approximately 2.828428 times more expressed than the other - as for arbitrary thresholds go, you can't go much more arbitrary than this.

ADD COMMENTlink written 2.1 years ago by h.mon29k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1448 users visited in the last hour