EdgeR exactTest - treatment names determine sign of fold change

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Spollen, William G. ▴ 30

@spollen-william-g-5281

Last seen 9.0 years ago

United States

Hi I am still new to EdgeR and am using it to do pairwise comparisons of RNA seq data. I just realized that the sign of the fold change will be determined by how you label the samples in groups. So if I have T1 and T2 as my two groups, it is labeled in that order in d$samples, and in the levels reported in d$samples$group. If I use as names T80 and T60 d$samples will list them in that order but the levels in d$samples$group will sort them and that changed the sign of the fold change. I am using the same input file each time. All else is the same, I just changed the labels I used for the samples. The code for exactTest seems to bear this out, using the levels of d$samples$group to determine how to take the ratio. Thought I should report that as I was looping through a list of comparisons and wondered why the sign changed. I am using v2.6.2 EdgeR. Thanks Bill [[alternative HTML version deleted]]

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ADD COMMENT • link updated 13.5 years ago by Mark Robinson ▴ 880 • written 13.5 years ago by Spollen, William G. ▴ 30

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Mark Robinson ▴ 880

@mark-robinson-4908

Last seen 7.0 years ago

Hi Bill, You can control this with the 'pair' argument in your call to exactTest(). Have a look at the description in ?exactTest Best, Mark ---------- Prof. Dr. Mark Robinson Bioinformatics Institute of Molecular Life Sciences University of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland v: +41 44 635 4848 f: +41 44 635 6898 e: mark.robinson at imls.uzh.ch o: Y11-J-16 w: http://tiny.cc/mrobin On 11.05.2012, at 22:12, Spollen, William G. wrote: > Hi > > I am still new to EdgeR and am using it to do pairwise comparisons of RNA seq data. I just realized that the sign of the fold change will be determined by how you label the samples in groups. So if I have T1 and T2 as my two groups, it is labeled in that order in d$samples, and in the levels reported in d$samples$group. If I use as names T80 and T60 d$samples will list them in that order but the levels in d$samples$group will sort them and that changed the sign of the fold change. I am using the same input file each time. All else is the same, I just changed the labels I used for the samples. The code for exactTest seems to bear this out, using the levels of d$samples$group to determine how to take the ratio. > > Thought I should report that as I was looping through a list of comparisons and wondered why the sign changed. I am using v2.6.2 EdgeR. > > Thanks > > Bill > > > [[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 COMMENT • link 13.5 years ago Mark Robinson ▴ 880

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Yes, I saw that. But in the context of a loop where you make the 6 pairwise comparisons of 4 group members it becomes important to name your groups in either asending or descending order to keep the fold changes consistent. I just wanted to alert anybody else in my situation to this possible source of trouble. Thanks Bill ________________________________________ From: Mark Robinson [mark.robinson@imls.uzh.ch] Sent: Saturday, May 12, 2012 2:20 AM To: Spollen, William G. Cc: bioconductor at r-project.org Subject: Re: [BioC] EdgeR exactTest - treatment names determine sign of fold change Hi Bill, You can control this with the 'pair' argument in your call to exactTest(). Have a look at the description in ?exactTest Best, Mark ---------- Prof. Dr. Mark Robinson Bioinformatics Institute of Molecular Life Sciences University of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland v: +41 44 635 4848 f: +41 44 635 6898 e: mark.robinson at imls.uzh.ch o: Y11-J-16 w: http://tiny.cc/mrobin On 11.05.2012, at 22:12, Spollen, William G. wrote: > Hi > > I am still new to EdgeR and am using it to do pairwise comparisons of RNA seq data. I just realized that the sign of the fold change will be determined by how you label the samples in groups. So if I have T1 and T2 as my two groups, it is labeled in that order in d$samples, and in the levels reported in d$samples$group. If I use as names T80 and T60 d$samples will list them in that order but the levels in d$samples$group will sort them and that changed the sign of the fold change. I am using the same input file each time. All else is the same, I just changed the labels I used for the samples. The code for exactTest seems to bear this out, using the levels of d$samples$group to determine how to take the ratio. > > Thought I should report that as I was looping through a list of comparisons and wondered why the sign changed. I am using v2.6.2 EdgeR. > > Thanks > > Bill > > > [[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

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