Question: Can logFC be used to determine effect size?
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6.2 years ago by
Guest User12k
Guest User12k wrote:
Hello, I am trying to work out the meaning of logFC in the toptable from limma package. Some sources say that it is the log2 of FC and others say that it is not. Is this value the actual difference in averages of cases and controls (and as such can it be used to determine effect size)? Regards, Jack -- output of sessionInfo(): R version 2.15.2 Patched (2012-11-28 r61176) -- Sent via the guest posting facility at bioconductor.org.
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ADD COMMENTlink modified 9 months ago by Bioconductor Community ♦♦ 0 • written 6.2 years ago by Guest User12k
Answer: Can logFC be used to determine effect size?
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gravatar for James W. MacDonald
6.2 years ago by
United States
James W. MacDonald51k wrote:
Hi Jack, On 8/9/2013 5:02 AM, Jack [guest] wrote: > Hello, > I am trying to work out the meaning of logFC in the toptable from limma package. Some sources say that it is the log2 of FC and others say that it is not. The logFC column is a coefficient from your model (or the numerator from a contrast). If you have set things up correctly, it will be the log2 of FC between two or more sample types. In other words, if you are doing a simple case vs control, and you specify the model correctly and select the proper coefficient for your topTable(), then the logFC will be the log fold change between the two groups. And note that log(A/B) = log(A) - log(B), and what you are doing with limma is usually taking logged data and computing the difference in means. So you are computing the right hand side of that equation, but it is identical to the left hand side. Best, Jim > > Is this value the actual difference in averages of cases and controls (and as such can it be used to determine effect size)? > > Regards, > Jack > > -- output of sessionInfo(): > > R version 2.15.2 Patched (2012-11-28 r61176) > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
ADD COMMENTlink written 6.2 years ago by James W. MacDonald51k
Answer: Can logFC be used to determine effect size?
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gravatar for Gordon Smyth
6.2 years ago by
Gordon Smyth38k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth38k wrote:

The best way to find out what something means is to read the documentation. If you want to know what logFC is from toptable, then open the help page help("toptable") and scan down for the entry for logFC, which says:

"logFC: estimate of the log2-fold-change corresponding to the effect or contrast"

Every output quantity is carefully documented in this way.

What sources say that logFC is not the log2 fold-change?

Gordon

ADD COMMENTlink modified 9 months ago • written 6.2 years ago by Gordon Smyth38k
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