Question: edgeR logFC
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6.8 years ago by
Christopher T Gregg210 wrote:
Hello, I just need someone to clarify whether the logFC column in the toptags dataframe is log base 2 or log base 10. I was unable to see this information in the manuals. Thank you very much. best wishes, Chris [[alternative HTML version deleted]]
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modified 6.8 years ago by Gordon Smyth39k • written 6.8 years ago by Christopher T Gregg210
0
6.8 years ago by
Scripps Research, La Jolla, CA
Ryan C. Thompson7.4k wrote:
Looking in the code for glmLRT, I see this line: logFC <- drop((glmfit$coefficients %*% contrast)/log(2)) Which looks like the formula for changing the logarithm base from e to 2. So I believe logFC is reported in base 2. On Mon 14 Jan 2013 05:27:40 PM PST, chris_utah wrote: > Hello, > > I just need someone to clarify whether the logFC column in the toptags dataframe is log base 2 or log base 10. I was unable to see this information in the manuals. > > Thank you very much. > > best wishes, > Chris > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor ADD COMMENTlink written 6.8 years ago by Ryan C. Thompson7.4k Answer: edgeR logFC 0 6.8 years ago by Gordon Smyth39k Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia Gordon Smyth39k wrote: Or else look at the help page for glmLRT, which says: "The data frame table contains the following columns: logFC: log2-fold change of expression between conditions being tested." In edgeR, all fold changes are stored internally in natural log, meaning that fit$coefficient valuas are natural log, but all fold changes that are presented in output tables or stored in fit$table components are log2. Best wishes Gordon > Date: Mon, 14 Jan 2013 17:32:42 -0800 > From: "Ryan C. Thompson" <rct at="" thompsonclan.org=""> > To: chris_utah <chris.gregg at="" neuro.utah.edu=""> > Cc: bioconductor at r-project.org > Subject: Re: [BioC] edgeR logFC > > Looking in the code for glmLRT, I see this line: > > logFC <- drop((glmfit$coefficients %*% contrast)/log(2)) > > Which looks like the formula for changing the logarithm base from e to > 2. So I believe logFC is reported in base 2. > > On Mon 14 Jan 2013 05:27:40 PM PST, chris_utah wrote: >> Hello, >> >> I just need someone to clarify whether the logFC column in the toptags >> dataframe is log base 2 or log base 10. I was unable to see this >> information in the manuals. >> >> Thank you very much. >> >> best wishes, >> Chris >> ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}
Thank you, Gordon. I appreciate you helping to clarify this for me. best wishes, Chris On Jan 15, 2013, at 4:30 PM, Gordon K Smyth wrote: > Or else look at the help page for glmLRT, which says: > > "The data frame table contains the following columns: > logFC: log2-fold change of expression between conditions being tested." > > In edgeR, all fold changes are stored internally in natural log, meaning that fit$coefficient valuas are natural log, but all fold changes that are presented in output tables or stored in fit$table components are log2. > > Best wishes > Gordon > >> Date: Mon, 14 Jan 2013 17:32:42 -0800 >> From: "Ryan C. Thompson" <rct@thompsonclan.org> >> To: chris_utah <chris.gregg@neuro.utah.edu> >> Cc: bioconductor@r-project.org >> Subject: Re: [BioC] edgeR logFC >> >> Looking in the code for glmLRT, I see this line: >> >> logFC <- drop((glmfit\$coefficients %*% contrast)/log(2)) >> >> Which looks like the formula for changing the logarithm base from e to >> 2. So I believe logFC is reported in base 2. >> >> On Mon 14 Jan 2013 05:27:40 PM PST, chris_utah wrote: >>> Hello, >>> >>> I just need someone to clarify whether the logFC column in the toptags dataframe is log base 2 or log base 10. I was unable to see this information in the manuals. >>> >>> Thank you very much. >>> >>> best wishes, >>> Chris >>> > > ______________________________________________________________________ > The information in this email is confidential and inte...{{dropped:25}}