[BioC] EdgeR exactTest - treatment names determine sign of fold change

[Mark Robinson]

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

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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
> 
> 
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