What about this example: (generated with write.table(as.data.frame(resSig[
order( -resSig$log2FoldChange, -resSig$baseMean ),]),
          file="UpRegulated.txt")

   transcript_ID baseMean log2FoldChange  c99091_g1_i2 433.9095957
4.454648409  c94900_g1_i2 81.89590041 -4.621788185  c95454_g1_i2 85.99069543
-4.714932567  c86874_g1_i2 89.26653144 -4.784367099  c106856_g1_i5
89.26653144 -4.784367099  c104937_g1_i2 89.26653144 -4.784367099
c98144_g1_i2 93.36132646 -4.865963134  c95410_g1_i3 94.99924447 -4.897496825
c103032_g2_i2 97.45612148 -4.943692641  c108287_g1_i4 102.3698755
-5.032327057  c107571_g3_i3 110.5594655 -5.169976643  c96989_g1_i1
140.0419897 -5.583327146  c96989_g1_i5 157.2401288 -5.779465439
c94096_g1_i2 203.920792 -6.201318372  c99876_g1_i3 229.3085211 -6.382470134
c104215_g2_i4 262.0668813 -6.580890544  c78891_g2_i1 273.5323074
-6.642674841  c96726_g1_i3 337.4111097 -6.932019693  c92607_g2_i3
386.5486499 -7.106787095  c91544_g1_i1 420.1259691 -7.208392858

Only the first one is up-regulated and the rest are down?

Thanks,
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 Sun, May 25, 2014 at 9:22 PM, Michael Love
<michaelisaiahlove@gmail.com>wrote:

> Hi Alicia,
>
> Positive log fold change for SP vs EB means up-regulated in SP.
>
> Negative log fold change means down-regulated in SP.
>
> Mike
> On May 25, 2014 7:40 PM, "Alicia R. Pérez-Porro" <
> alicia.r.perezporro@gmail.com> wrote:
>
>> Dear community,
>>
>> I am using DESeq2 to perform my differential expression analyses. My
>> question is, I think, very simple. To interprete the results if I have:
>>
>> > mcols(res, use.names=TRUE) ##To know the level of conditions
>> DataFrame with 6 rows and 2 columns
>>                        type                                description
>>                 <character>                                <character>
>> baseMean       intermediate                the base mean over all rows
>> log2FoldChange      results log2 fold change (MAP): condition SP vs EB
>> lfcSE               results         standard error: condition SP vs EB
>> stat                results         Wald statistic: condition SP vs EB
>> pvalue              results      Wald test p-value: condition SP vs EB
>> padj                results                       BH adjusted p-values
>>
>> By exporting my up-regulated genes doing:
>>
>> write.table(as.data.frame(resSig[ order( -resSig$log2FoldChange,
>> -resSig$baseMean ),]),
>>           file="UpRegulated.txt")
>>
>> Are my genes up-regulated in the EB condition? or in the SP condition?
>>
>> Thanks for your time.
>> Best,
>> 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
>>
>>         [[alternative HTML version deleted]]
>>
>>
>> _______________________________________________
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>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>

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