[BioC] DESeq2: up- and down-regulated genes

[Michael Love]

On Mon, May 26, 2014 at 12:18 PM, Alicia R. Pérez-Porro
<alicia.r.perezporro at gmail.com> wrote:
> Thanks!
>
> Just one last thing. I just did results(dds, contrast = c("condition", "NR",
> "DT")) and the number of most significant genes is the same as before (e.g.
> NRvsDT = DTvsNR) so I am assuming that the only thing that I am doing by
> specifying contrast is changing the polarity (what was -log2FC now is
> positive, and the opposite).

Yes, you've got it.

> But my list of genes is exactly the same. Am I
> understanding this correctly? So let's say that I have NR vs DT, whatever is
> log2FC is up-regulated in NR or what is the same, down-regulated in DT; and
> whatever is -log2FC is down-regulated in NR but up-regulated in DT, right?
>
> Thanks again for your patience and time.
> Alicia
>
>
>
> --
> Alicia R. Pérez-Porro
> PhD candidate
>
> Giribet lab
> Department of Organismic and Evolutionary Biology
> MCZ labs
> Harvard University
> 26 Oxford St, Cambridge MA 02138
> phone: +1 617-496-5308
> fax: +1 617-495-5667
> www.oeb.harvard.edu/faculty/giribet/
>
> Department of Marine Ecology
> Center for Advanced Studies of Blanes (CEAB-CSIC)
> C/Accés Cala St. Francesc 14
> 17300 Blanes, Girona, SPAIN
> phone: +34 972 336 101
> fax: +34 972 337 806
> www.ceab.csic.es
>
>
> On Mon, May 26, 2014 at 12:09 PM, Michael Love <michaelisaiahlove at gmail.com>
> wrote:
>>
>> hi Alicia,
>>
>> On Mon, May 26, 2014 at 12:04 PM, Alicia R. Pérez-Porro
>> <alicia.r.perezporro at gmail.com> wrote:
>> > Hi,
>> >
>> > I am trying to do:
>> >
>> >> res <- results( dds, contrast = list( "condition", "NR", "DT" ) )
>> >
>>
>> Just change list() to c() in the above:
>>
>> results(dds, contrast = c("condition", "NR", "DT"))
>>
>> > Error in results(dds, contrast = list("condition", "NR", "DT")) :
>> >   'contrast', as a list, should have length 2,
>> > see the manual page of ?results for more information
>> >
>> > And it's giving me an error :(
>> >
>> >
>> >
>> > --
>> > Alicia R. Pérez-Porro
>> > PhD candidate
>> >
>> > Giribet lab
>> > Department of Organismic and Evolutionary Biology
>> > MCZ labs
>> > Harvard University
>> > 26 Oxford St, Cambridge MA 02138
>> > phone: +1 617-496-5308
>> > fax: +1 617-495-5667
>> > www.oeb.harvard.edu/faculty/giribet/
>> >
>> > Department of Marine Ecology
>> > Center for Advanced Studies of Blanes (CEAB-CSIC)
>> > C/Accés Cala St. Francesc 14
>> > 17300 Blanes, Girona, SPAIN
>> > phone: +34 972 336 101
>> > fax: +34 972 337 806
>> > www.ceab.csic.es
>> >
>> >
>> > On Mon, May 26, 2014 at 11:42 AM, Simon Anders <anders at embl.de> wrote:
>> >
>> >> Hi Alicia
>> >>
>> >> On 26/05/14 17:20, Alicia R. Pérez-Porro wrote:
>> >>
>> >>>  1. MostSigGenes.txt, DownRegulated.txt and UpRegulated.txt always
>> >>> have
>> >>>
>> >>>     the same number of genes. This is confusing for me.
>> >>>
>> >>
>> >> This is because in all three cases, it is the same table. You only
>> >> change
>> >> the ordering of rows.
>> >>
>> >> Here, you take the table with all genes ("res") and reduce it to only
>> >> those rows with padj < 0.1:
>> >>
>> >>
>> >> > resSig <- res[ which(res$padj < .1), ]
>> >>
>> >> and in your "write.table" commands, you always write out this table,
>> >> but
>> >> you re-order the rows. (The "order" function gives the order of rows to
>> >> get
>> >> them sorted according to what you specify)
>> >>
>> >>   2. I understand then that maybe is better to only generate
>> >>>
>> >>>     MostSigGenes.txt and then divide the result in 2 txt files: one
>> >>> with
>> >>>     positive log2FC = upregulated and the other with negative log2FC =
>> >>>     downregulated, right?
>> >>>
>> >>
>> >> Probably, yes.
>> >>
>> >> Depends, though, on what you want to do with the text files afterwards.
>> >> If
>> >> you want to look at them in Excel and this is the tool you feel most
>> >> comfortable with, you could also simply write out the "resSig" table as
>> >> is,
>> >> with
>> >>   write.table( resSig, file="allSig.txt" )
>> >> or even the whole result table ('res' isntead of 'resSig') and do all
>> >> your
>> >> filtering and sorting in Excel.
>> >>
>> >>
>> >>   3. I don't understand with if I am entering the conditions like
>> >>>
>> >>>     "condition = factor(c("SP", "SP", "EB", "EB")))" then is comparing
>> >>>     EB vs. SP. I would have thought the opposite.
>> >>>
>> >>
>> >> R has the habit of sorting the names of the factor level by alphabet if
>> >> you don't explicitly tell it the order you want. And then, DESeq2
>> >> compares
>> >> by default the alphabetically last versus the first.
>> >>
>> >> If you want something else, just tell it what you want:
>> >>
>> >>   res <- results( dds, contrast = list( "condition", "EP", "SP" ) )
>> >>
>> >> to compare SP versus EP.
>> >>
>> >>   Simon
>> >>
>> >
>> >         [[alternative HTML version deleted]]
>> >
>> >
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