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

Michael Love michaelisaiahlove at gmail.com
Mon May 26 18:09:58 CEST 2014


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
>>
>
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>
>
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